Antibodies to MUC16 and methods of use thereof

ABSTRACT

The invention provides antibodies, and antigen-binding fragments thereof, that specifically bind to a polypeptide, or antigenic portion thereof, wherein the polypeptide is selected from a) MUC16 ectodomain polypeptide, b) MUC16 cytoplasmic domain polypeptide, and c) MUC16 extracellular domain polypeptide that contains a cysteine loop polypeptide. The invention&#39;s antibodies and compositions containing them are useful in diagnostic and therapeutic applications for diseases in which MUC16 is overexpressed, such as cancer.

This application is a divisional of U.S. patent application Ser. No.14/850,675, filed Sep. 10, 2015, issued as U.S. Pat. No. 9,790,283,which is a divisional of U.S. patent application Ser. No. 13/635,090,issued as U.S. Pat. No. 9,169,328, national stage of InternationalApplication No. PCT/US2011/030025, filed Mar. 25, 2011, which claimsbenefit of U.S. Provisional Application No. 61/317,964, filed Mar. 26,2010, each of which is hereby incorporated herein by reference in itsentirety for all purposes.

This invention was made with government support under grant numberCA052477 awarded by the National Institutes of Health. The governmenthas certain rights in the invention.

FIELD OF THE INVENTION

The invention relates to antibodies, and antigen-binding fragmentsthereof, that specifically bind to a polypeptide, or antigenic portionthereof, wherein the polypeptide is selected from a) MUC16 ectodomainpolypeptide, b) MUC16 cytoplasmic domain polypeptide, and c) MUC16extracellular domain polypeptide that contains a cysteine looppolypeptide. The invention's antibodies and compositions containing themare useful in diagnostic and therapeutic applications for diseases inwhich MUC16 is overexpressed, such as cancer.

BACKGROUND OF THE INVENTION

Cell surface markers and shed antigens are used in the diagnosis ofseveral cancers. For example, the CA125 antigen, recognized by the OC125antibody, is a tissue-specific, circulating antigen expressed in ovariancancer. The CA125 antigen is encoded by the MUC16 gene, cloned by Lloydand Yin. The full-length gene describes a complex tethered mucin proteinpresent primarily in a variety of gynecologic tissues, especiallyneoplasms. OC125 and other related antibodies react withglycosylation-dependent antigens present exclusively in the cleavedportion of the molecule.

A serum assay can detect elevated levels of the circulating CA125antigen in many epithelial ovarian cancer patients, and this antigen,derived using the ovarian cell line OVCA433, is recognized by the OC125antibody (1-2). The detection of circulating CA125 in serum has provento be a useful tool for the management of ovarian cancer patients andclinical trials (3-4). However, CA125 is neither sufficiently sensitivenor specific for general cancer screening (5-6). A variety of CA125linked antibodies including VK8 and M11 have subsequently been definedas present on ovarian cancer cells (7-9). Although these antibodies havebeen used to develop serum assays and various other studies in ovariancancer, they have significant shortcomings for clinical use in screeningor tissue delivery. These antibodies are not useful as screening tools,nor can they detect the proximal residual MUC16 protein fragment aftercleavage. This has limited their diagnostic and therapeuticapplications.

For example, OC125, M11, and most other antibodies prepared againstovarian cancer cell extracts are directed at complex,glycosylation-dependent antigens. These antigens are exclusively presentin the shed portion of MUC16 and cannot be employed to follow thebiology of the proximal portion of MUC16 and may not accurately reflecttissue distribution since the glycosylation patterns can varysubstantially among tissues. Because the vast majority of MUC16-reactiveantibodies, including OC125, react with the glycosylation-dependentantigen present exclusively in the cleaved portion of the molecule, thetrue distribution of MUC16 expression is not known (21). There iscurrently no antibody available to track the fate of the remaining MUC16protein fragment after cleavage and CA125 release.

Thus, there remains a need for the identification of antibodies that aredirected against sequences in the peptide backbone of MUC16, and thatare useful for diagnosis and treatment of cancers in which MUC16 isexpressed and/or overexpressed.

SUMMARY OF THE INVENTION

The invention provides an antibody, or an antigen-binding fragmentthereof, that specifically binds to a polypeptide, or antigenic portionthereof, wherein the polypeptide is selected from the group of a) MUC16ectodomain polypeptide, b) MUC16 cytoplasmic domain polypeptide, and c)MUC16 extracellular domain polypeptide that contains a cysteine looppolypeptide CQVSTFRSVPNRHHTGVDSLC (SEQ ID NO: 19). In one embodiment,the antibody internalizes into a cell. While not intending to limit theinvention to a particular sequence of MUC16 ectodomain, in oneembodiment, the MUC16 ectodomain polypeptide comprises a polypeptideselected from the group of Polypeptide 1 NFSPLARRVDRVAIYEE (SEQ IDNO:01) and Polypeptide 2 TLDRSSVLVDGYSPNRNE (SEQ ID NO:02). In anotherembodiment, the antibody lacks specific binding to a glycosylated MUC16extracellular domain. In yet a further embodiment, the antibodyspecifically binds to the Polypeptide 2 (SEQ ID NO:02) of the MUC16ectodomain polypeptide, and wherein the antibody comprises a variableheavy (V_(H)) chain encoded by SEQ ID NO:06, and a variable light(V_(L)) chain encoded by SEQ ID NO:07. In yet another alternativeembodiment, the antibody specifically binds to the Polypeptide 2 (SEQ IDNO:02) of the MUC16 ectodomain polypeptide, and wherein the antibodycomprises a variable heavy (V_(H)) chain encoded by SEQ ID NO:04, and avariable light (V_(L)) chain encoded by SEQ ID NO:05. In a furtherembodiment, the antibody specifically binds to the Polypeptide 1 (SEQ IDNO:01) of the MUC16 ectodomain polypeptide, and wherein the antibodycomprises a variable heavy (V_(H)) chain encoded by SEQ ID NO:08, and avariable light (V_(L)) chain encoded by at least one of SEQ ID NO:09 andSEQ ID NO: 10. In one embodiment, the MUC16 cytoplasmic domainpolypeptide comprises VTTRR RKKEGEYNVQ QQ (SEQ ID NO:18). Morepreferably, but without limitation, the MUC16 cytoplasmic domainpolypeptide comprises Polypeptide 3 CGVLVTTRRRKKEGEYNVQQQ (SEQ IDNO:03). In an alternative embodiment, the MUC16 extracellular domainpolypeptide that contains a cysteine loop polypeptide comprisesCQVSTFRSVPNRHHTGVDSLC (SEQ ID NO: 19). More preferably, but withoutlimitation, the MUC16 extracellular domain polypeptide comprisesPolypeptide 4 KSYF SDCQVSTFRS VPNRHHTGVD SLCNFSPL (SEQ ID NO:15). In yetanother alternative embodiment, the antibody specifically binds to thePolypeptide 4 (SEQ ID NO: 15) of the MUC16 extracellular domainpolypeptide, and wherein the antibody comprises a variable heavy (V_(H))chain encoded by SEQ ID NO: 11, and a variable light (V_(L)) chainencoded by SEQ ID NO: 12. In a further alternative embodiment, theantibody is selected from the group of a chimeric antibody, a monoclonalantibody, a recombinant antibody, an antigen-binding fragment of arecombinant antibody, a humanized antibody, and an antibody displayedupon the surface of a phage. In another embodiment, the antigen-bindingfragment is selected from the group of a Fab fragment, a F(ab′)2fragment, and a Fv fragment. In an alternative embodiment, the antibody,or antigen-binding fragment thereof, is covalently linked to a cytotoxicagent or a prodrug of a cytotoxic agent. In a preferred embodiment, theantibody is a monoclonal antibody produced by a hybridoma cell line.

The invention also provides an isolated monoclonal antibody, or anantigen-binding fragment thereof, produced by a hybridoma cell line,wherein the antibody specifically binds to a polypeptide, or antigenicportion thereof, wherein the polypeptide is selected from the group ofa) MUC16 ectodomain polypeptide, b) MUC16 cytoplasmic domainpolypeptide, and c) MUC16 extracellular domain polypeptide that containsa cysteine loop polypeptide CQVSTFRSVPNRHHTGVDSLC (SEQ ID NO:19). In oneembodiment, the MUC16 ectodomain polypeptide comprises Polypeptide 1(SEQ ID NO:01) and the antibody is selected from the group of9B11.20.16, 10A2, 2F4, 23D3, 30B1, and 31B2. In an alternativeembodiment, the MUC16 ectodomain polypeptide comprises Polypeptide 2(SEQ ID NO:02), and wherein the antibody is selected from the group of4H11.2.5, 13H1, 29G9, 9C9.21.5.13, 28F8, 23G12, 9C7.6, 11B6, 25G4,5C2.17, 4C7, 26B2, 4A5.37, 4A2, 25H3, and 28F7.18.10. In yet a furtherembodiment, the MUC16 cytoplasmic domain polypeptide comprisesPolypeptide 3 CGVLVTTRRRKKEGEYNVQQQ (SEQ ID NO:03), and wherein theantibody is selected from the group of 31A3.5.1, 19D1, 10F6, 22E10,22F1, 3H8, 22F11, 4D7, 24G12, 19G4, 9A5, 4C2, 31C8, 27G4, and 6H2. Inanother alternative embodiment, the MUC16 extracellular domainpolypeptide comprises Polypeptide 4 KSYF SDCQVSTFRS VPNRHHTGVD SLCNFSPL(SEQ ID NO:15), and wherein the antibody is selected from the group of24B3 and 9C7.

The invention additionally provides a composition comprising (a) any oneor more of the antibodies, or antigen-binding fragments thereof, thatare described herein, and (b) a pharmaceutically acceptable carrier.

Also provided by the invention is a hybridoma cell line that produces amonoclonal antibody that specifically binds to a polypeptide, orantigenic portion thereof, selected from the group of a) MUC16ectodomain polypeptide, b) MUC16 cytoplasmic domain polypeptide, and c)MUC16 extracellular domain polypeptide that contains a cysteine looppolypeptide CQVSTFRSVPNRHHTGVDSLC (SEQ ID NO:19).

The invention additionally provides a method for detecting a diseasethat comprises overexpression of MUC16 in a subject, comprising a)providing i) a sample from a subject, and ii) any one or more of theantibodies, or antigen-binding fragments thereof, that are describedherein, b) contacting the sample with the antibody under conditions forspecific binding of the antibody with its antigen, and c) detecting anincreased level of binding of the antibody to the sample compared to acontrol sample lacking the disease, thereby detecting the disease in thesubject. In one embodiment, the disease is cancer. In a preferredembodiment, the cancer is selected from the group of ovarian cancer andbreast cancer. While not intending to limit the method of detection, inone embodiment, detecting binding of the antibody to the sample isimmunohistochemical, enzyme-linked immunosorbent assay (ELISA),fluorescence-activated cell sorting (FACS), Western blot,immunoprecipitation, and/or radiographic imaging.

Also provided herein is a method for treating a disease that comprisesoverexpression of MUC16, comprising administering to a subject havingthe disease a therapeutically effective amount of any one or more of theantibodies, or antigen-binding fragments thereof, that are describedherein. In one embodiment, the disease is cancer, as exemplified byovarian cancer and breast cancer.

The invention also provides an isolated antibody, or an antigen-bindingfragment thereof, that specifically binds to a MUC16 polypeptide or toan antigenic portion thereof, wherein the MUC16 polypeptide is selectedfrom the group of a) TLDRKSVFVDGYSQNRDD (SEQ ID NO:21), b)KSYFSDCQVLAFRSVSNNNNHTGVDSLCNFSPL (SEQ ID NO:22), c)SLYSNCRLASLRPKKNGTATGVNAICSYHQN (SEQ ID NO:23), d) KSYFSDCQVNNFRS (SEQID NO: 30), and e) TLDRSSVLVDGYSQNRDD (SEQ ID NO: 31). In oneembodiment, the antibody is selected from the group of a monoclonalantibody, a chimeric antibody, a recombinant antibody, anantigen-binding fragment of a recombinant antibody, a humanizedantibody, and an antibody displayed upon the surface of a phage. In apreferred embodiment, the antibody is a monoclonal antibody produced byhybridoma cells selected from the group of 12B10-3G10, 10C4-3H5,10C4-1F2, 10C4-2H8, 10C4-1G7, 17F2-3G5, 17F2-3F6, 17F2-2F9, 17F2-1E11,12B10-3F7, 12B10-2F6, 12B10-2F10, 25E9-3, 25E9-5, 25E9-1, 25E9-16,21B8-1H11, 21B8-3G6, 21B8-3H9, 21B8-1G8, 21E1-1E3, 21E1-1G9, 21E1-2G7,21E1-3G12, 4H1-2E1, 4H1-2E3, 4H1-3E1, 4H1-3H3, 15A8-2E2, 15A8-2E10,15A8-2E11, 15A8-3D2, 22B5-1F6, 22B5-3G9, 22B5-2G8, and 22B5-3F11. In aparticular embodiment, the MUC16 polypeptide is TLDRKSVFVDGYSQNRDD (SEQID NO:21), and the antibody comprises a variable heavy (V_(H)) chainsequence SEQ ID NO:27, and a variable light (V_(L)) chain sequence SEQID NO:29, such as the monoclonal antibody produced by hybridoma cell12B10-3G10. In an alternative embodiment, the antigen-binding fragmentis selected from the group of a Fab fragment, a F(ab′)2 fragment, and aFv fragment. In a more preferred embodiment, the antibody, orantigen-binding fragment thereof, is covalently linked to a cytotoxicagent and/or to a prodrug of a cytotoxic agent. In a further embodiment,the antibody specifically binds to human MUC16 (SEQ ID NO:25). Inanother embodiment, the antibody internalizes into a cell. In analternative embodiment, the antibody lacks specific binding to aglycosylated MUC16 extracellular domain.

The invention also provides a composition comprising (a) any one or moreof the invention's antibodies and/or antigen-binding fragments thereof,and (b) a pharmaceutically acceptable carrier.

The invention further provides a hybridoma cell that produces anantibody, or an antigen-binding fragment thereof, that specificallybinds to a MUC16 polypeptide or to an antigenic portion thereof, whereinthe MUC16 polypeptide is selected from the group of a)TLDRKSVFVDGYSQNRDD (SEQ ID NO:21), b) KSYFSDCQVLAFRSVSNNNNHTGVDSLCNFSPL(SEQ ID NO:22), c) SLYSNCRLASLRPKKNGTATGVNAICSYHQN (SEQ ID NO:23), d)KSYFSDCQVNNFRS (SEQ ID NO: 30), and e) TLDRSSVLVDGYSQNRDD (SEQ ID NO:31).

The invention also provides an isolated nucleotide sequence comprising apolynucleotide that encodes at least one of a variable heavy (V_(H))chain sequence and the variable light (V_(L)) chain sequence of anantibody that specifically binds to a MUC16 polypeptide, wherein theMUC16 polypeptide is selected from the group of a) TLDRKSVFVDGYSQNRDD(SEQ ID NO:21), b) KSYFSDCQVLAFRSVSNNNNHTGVDSLCNFSPL (SEQ ID NO:22), c)SLYSNCRLASLRPKKNGTATGVNAICSYHQN (SEQ ID NO:23), d) KSYFSDCQVNNFRS (SEQID NO: 30), and e) TLDRSSVLVDGYSQNRDD (SEQ ID NO: 31). In oneembodiment, the MUC16 polypeptide is TLDRKSVFVDGYSQNRDD (SEQ ID NO:21)and the polynucleotide encoding the variable heavy (V_(H)) chainsequence comprises SEQ ID NO:26, and wherein the polynucleotide encodingthe variable light (V_(L)) chain sequence comprises SEQ ID NO:28.

The invention also provides a method for producing an antibody thatspecifically binds to a MUC16 polypeptide or to an antigenic portionthereof, comprising administering to a subject an immunologicallyeffective amount of a MUC16 polypeptide selected from the group of a)TLDRKSVFVDGYSQNRDD (SEQ ID NO:21), b) KSYFSDCQVLAFRSVSNNNNHTGVDSLCNFSPL(SEQ ID NO:22), c) SLYSNCRLASLRPKKNGTATGVNAICSYHQN (SEQ ID NO:23), d)KSYFSDCQVNNFRS (SEQ ID NO: 30), and e) TLDRSSVLVDGYSQNRDD (SEQ ID NO:31).

The invention additionally provides a method for identifying a subjectas having disease, comprising determining the level, in a sample fromthe subject, of specific binding of any one or more of the invention'santibodies and/or antigen-binding fragments thereof, with the MUC16polypeptide or with the antigenic portion thereof, wherein detecting analtered level of the specific binding relative to a control sampleidentifies the subject as having disease. In one embodiment, the diseaseis cancer exemplified by ovarian cancer and breast cancer. In anotherembodiment, the method further comprises detecting an altered level ofbinding of the antibody to the sample compared to a control sample.Optionally, the detecting is selected from the group ofimmunohistochemistry, enzyme-linked immunosorbent assay (ELISA),fluorescence-activated cell sorting (FACS), Western blot,immunoprecipitation, and radiographic imaging.

The invention also provides a method for reducing one or more symptomsof disease comprising administering to a subject in need thereof atherapeutically effective amount of any one or more of the invention'santibodies and/or antigen-binding fragment thereof. In one embodiment,the disease is cancer, exemplified by ovarian cancer and breast cancer.Optionally, the method further comprises detecting a reduction in one ormore symptoms of the disease after the administration step.

BRIEF DESCRIPTION OF THE DRAWINGS

FIG. 1: Three MUC16 carboxy terminus peptides were synthesized at theMSKCC Microchemistry Core Facility. Polypeptide 1 is near the putativecleavage site, Polypeptide 2 is before the transmembrane, andPolypeptide 3 is the internal peptide, which is inside thetransmembrane.

FIG. 2: Comparison staining of high-grade serous ovarian carcinomasusing OC125 (left panel) and 4H11 (right panel)

FIGS. 3A-FIG. 3L: Immunohistochemical scoring of OC125 and 4H11 ontissue microarrays of high-grade ovarian serous carcinoma. Onlymembranous and/or cytoplasmic staining was considered positive. Score 0:No staining; Score 1: <5% strong or weak; Score 2: 5-50% strong or weak;Score 3: 51-75% strong or 51-100% weak; Score 4: 76-99% strong; Score 5:100% strong. FIG. 3A: OC125 (Score 0); FIG. 3B: OC125 (Score 1); FIG.3C: OC125 (Score 2); FIG. 3D: OC125 (Score 3); FIG. 3E: OC125 (Score 4);FIG. 3F: OC125 (Score 5); FIG. 3G: 4H11 (Score 0); FIG. 3H: 4H11 (Score1); FIG. 3I: 4H11 (Score 2); FIG. 3J: 4H11 (Score 3); FIG. 3K: 4H11(Score 4); FIG. 3L: 4H11 (Score 5).

FIG. 4A and FIG. 4B: Western blot analysis. FIG. 4A: Western blotanalysis of GST-ΔMUC16^(c114) fusion protein with monoclonal antibodies9C9.21.5.13 and 4H11.2.5. FIG. 4B: Western blot analysis ofSKOV3-phrGFP-ΔMUC16^(c114) and SKOV3-phrGFP-ΔMUC16^(c334) proteinextract and probed with monoclonal antibodies 9C9.21.5.13 and 4H11.2.5.

FIGS. 5A-5D: MUC16 carboxy terminus monoclonal antibodies bindingaffinity on OVCAR3 cells. FIG. 5E: Internalization of radio-labeled 4H11and OC125 monoclonal antibodies on SKOV3-phrGFP-ΔMUC16^(c334) stabletransfected cells.

FIG. 6A-D: Comparison staining intensities of OC125 and 4H11 monoclonalantibodies on tissue microarrays containing cancers of the prostate (2A,concordant), lung (2B, discordant), breast (2C, discordant), andpancreas (2D, discordant).

FIGS. 7A-7F: FACS analysis as described in the Material and Methodssection was performed with commercial antibodies and MUC16 carboxyterminus monoclonal antibodies on OVCAR3 wt, SKOV3-phrGFP-ΔMUC16^(c114)and SKOV3-phrGFP-ΔMUC16^(c334) stable transfected cell lines.

FIGS. 8A-8I: Nucleotide sequence encoding antibody variable heavy(V_(H)) chain and antibody variable light (V_(L)) chain. FIG. 8A: 4A5V_(H) (SEQ ID NO:04), FIG. 8B: 4A5 V_(L) (SEQ ID NO:05), FIG. 8C: 4H11V_(H) (SEQ ID NO:06), FIG. 8D: 4H11 V_(L) (SEQ ID NO:07), FIG. 8E: 9B11V_(H) (SEQ ID NO:08), FIG. 8F: 9B11 V_(L.A) (SEQ ID NO:09), FIG. 8G:9B11 V_(L.B) (SEQ ID NO: 10), FIG. 8H: 24B3 V_(H) (SEQ ID NO: 11), FIG.8I: 24B3 V_(L) (SEQ ID NO: 12).

FIGS. 9A-9F: Homo sapiens MUC16 (GenBank NP_078966) (SEQ ID NO: 13),FIG. 9G: Polypeptide 1 (SEQ ID NO:01), FIG. 9H: Polypeptide 2 (SEQ IDNO:02), FIG. 9I: Polypeptide 3 (SEQ ID NO:03), FIG. 9J: Transmembranedomain (SEQ ID NO:14), FIG. 9K: Polypeptide 4 (SEQ ID NO:15) containinga cysteine loop polypeptide (SEQ ID NO: 19).

FIG. 10: Schematic of MUC16 structure.

FIG. 11. Design and in vitro analysis of MUC-CD targeted CARs. (A)Schematic diagram of the first generation 4H11z and second generation4H11-28z retroviral vectors. 4H11scFv: MUC16 specific scFv derived fromthe heavy (V_(H)) and light (V_(L)) chain variable regions of themonoclonal antibody 4H11; CD8: CD8 hinge and transmembrane domains;CD28: CD28 transmembrane and cytoplasmic signaling domains; ζ chain: Tcell receptor ζ chain cytoplasmic signaling domain; LTR: long terminalrepeat; black box: CD8 leader sequence; grey box: (Gly₄Ser)₃ linker;arrows indicate start of transcription. (B) FACS analysis of human Tcells retrovirally transduced to express either the 4H11z or 19z1 CAR.(C) 4H11z⁺ but not 19z1⁺ T cells expand on 3T3(MUC-CD/B7.1) AAPC. CAR⁺were co-cultured on 3T3(MUC-CD/B7.1) AAPC monolayers at 3×10⁶ CAR⁺ Tcells/well of a 6 well plate. Proliferation of CAR⁺ T cells, normalizedto the CAR⁺ T cell fraction as assessed by FACS for the CAR⁺ fraction incombination with viable T cell counts obtained on days 2, 4 and 7, asassessed by trypan blue exclusion assays.

FIG. 12. In vitro comparison of T cells modified to express the firstgeneration 4H11z CAR to T cells modified to express the secondgeneration co-stimulatory 4H11-28z CAR. (A) CAR⁺ T cells wereco-cultured on MUC-CD monolayers with (right panel) or without B7.1(left panel). 3×10⁶ CAR⁺ T cells were co-cultured on AAPC monolayers in6 well tissue culture plates in cytokine-free medium. Total viable Tcell counts were assessed on days 2, 4 and 7, by trypan blue exclusionassays. 4H11-28z⁺ T cells markedly expanded when compared to 4H11z⁺ Tcells upon co-culture with 3T3(MUC-CD) AAPCs, **p=0.0023 (4H11z comparedto 4H11-28z). In contrast, both 4H11z⁺ and 4H11-28z⁺ T cells expandedsimilarly on 3T3(MUC-CD/B7.1) AAPCs, p=0.09, (4H111z compared to4H11-28z). Control 19-28z⁺ T cells did not proliferate on 3T3(MUC-CD),**p=0.0056 (19-28z compared to 4H11z), **p=0.0011 (19-28z compared to4H11-28z), or on 3T3(MUC-CD/B7.1), **p=0.0026 (19-28z compared to4H11z), **p=0.0087 (19-28z compared to 4H11-28z). (B) 4H11-28z⁺ but not4H11z⁺ T cells secrete IL-2 upon co-culture with 3T3(MUC-CD) AAPCs.Tissue culture supernatants at day 2 following activation on 3T3(MUC-CD)AAPCs were analyzed for cytokine secretion. 4H11-28z⁺ T cells, incontrast to 4H11z⁺ T cells, demonstrated enhanced secretion of IL-2consistent with T cell co-stimulation mediated through the 4H11-28z CAR.***p=0.0008 (19z11 or 19-28z compared to 4H11z), **p=0.0026 (19z11 or19-28z compared to 4H11-28z), **p=0.0046 (4H11z compared to 4H11-28z).Furthermore, both 4H11-28z⁺ and 4H11z⁺ T cells secreted IFNγ. *p=0.011(4H11z compared to 4H11-28z). Control 19z11 and 1928z transduced T cellsfailed to secrete either IL-2 or IFNγ. **p=0.0034 (19z11 compared to4H11z), **p=0.036 (19-28z compared to 4H11z), ***p=0.0008 (19-28zcompared to 4H11-28z). (C) Expansion of CAR⁺ T cells following 3 cyclesof stimulation on 3T3(MUC-CD/B7.1). Human T cells transduced to expresseither 4H11z or 4H11-28z CARs demonstrated a >2 log expansion over 2cycles of stimulation on 3T3(MUC-CD/B7.1) AAPCs. Arrows indicate 1st and2nd cycles of restimulation on AAPCs. (D) FACS analysis of the CAR⁺ Tcell fraction of 4H11-28z⁺ T cells increased following each weekly cycleof stimulation. (I) FACS following initial transduction, (II) FACS at 7days following first stimulation on AAPCs, (III) FACS at 7 daysfollowing second stimulation on AAPCs. These data are representative ofone of three different experiments using three different healthy donor Tcell populations, all of which demonstrated similar proliferation andcytokine secretion patterns.

FIG. 13. MUC-CD targeted T cells specifically expand and lyse MUC-CD⁺tumor cells. (A) Cytotoxicity assay of 4H11z⁺ and 4H11-28z⁺ T cellstargeting OV-CAR(MUC-CD) tumor cells demonstrates efficient cytotoxicitymediated by T cells from healthy donors modified to express the firstand second generation MUC-CD targeted CARs. Control T cells modified toexpress the first and second generation CD19-targeted 19z11 and 19-28zCARs failed to demonstrate significant lysis of target tumor cells. (B)Healthy donor T cells modified to express the 4H11-28z CAR equally lyseprimary patient ascites-derived MUC-CD⁺ tumor cells when compared to Tcells modified to express the control 19-28z CAR. This data represents 1or 3 experiments targeting primary tumor cells from 3 ovarian carcinomapatients with similar results. (C) Autologous T cells isolated fromperipheral blood, when modified with the 4H11-28z CAR, exhibitsignificant lysis of autologous MUC-CD⁺ ascites-derived tumor cells whencompared to control 19-28z⁺ autologous T cells. These data represent 1of 3 experiments utilizing T cells and autologous tumor cells from 3different ovarian carcinoma patients with similar results. (D) Antigenspecific proliferation of MUC-CD targeted CFSE labeled T cells afterco-culture with OV-CAR3(MUC-CD) tumor cells. CFSE labeled CAR⁺ T cellswere co-cultured with MUC-CD expressing OV-CAR3 tumor cells at 1:1 ratiofor 5 days. Proliferation of CFSE labeled T cells was assessed by FACSdemonstrating efficient proliferation of both 4H11z⁺ and 4H11-28z⁺ Tcells but not control 19-28z⁺ T cells. (E) CFSE results were furtherconfirmed by absolute T cell numbers assessed on days 2, 4 and 7following co-culture with OV-CAR3(MUC-CD) tumor cells. (F) FACS analysisof the expression of 4-1BBL on OVCAR3(MUC-CD) cells. OV-CAR3(MUC-CD)cells were stained with anti-human 4-1BBL antibody (thick line) or withisotype control (thin line). FACS analysis demonstrated expression of4-1BBL on OV-CAR3(MUC-CD) tumor cells. Further FACS analyses failed toreveal expression of the co-stimulatory ligands B7.1, B7.2, or OX-40L.

FIG. 14. Eradication of OV-CAR3(MUC-CD) tumors after intra-peritonealtreatment with first and second generation of MUC-CD targeted T cells.(A) Intraperitoneal injection of OV-CAR3(MUC-CD) tumors in untreatedSCID-Beige mice results in abdominal distension and nodular peritonealtumors. SCID-Beige mice were injected intraperitoneally with 3×10⁶OV-CAR3(MUC-CD) cells. At 5 weeks post intraperitoneal injection ofOV-CAR3(MUC-CD) tumor cells mice developed ascities as evidenced by adistended abdomen (center panel) when compared to a tumor free mouse(left panel). Post mortem visualization of the peritoneum demonstratesnodular tumor masses (arrows) within the abdominal cavity (right panel).(B) Intraperitoneal injection of 4H11z⁺ and 4H11-28z⁺ T cells eitherdelay tumor progression or fully eradicate disease. Kaplan-Meiersurvival curve of SCID-Beige mice treated with first or secondgeneration of MUC-CD targeted T cells. SCID-Beige mice were infused ipwith 3×10⁶ OV-CAR3(MUC-CD) tumor cells on day 1 followed by 3×10⁷ 4H11z⁺or 4H11-28z⁺ T cells on day 2. All untreated mice or mice treated withcontrol 19z1⁺ T cells developed established tumors and were sacrificedby day 50. In contrast, 27% of mice treated with either 4H11 z⁺ or4H11-28z⁺ T cells remained without clinical evidence of disease by day120. *p=0.01 (4H11z compared to 19z11), **p=0.0023 (4H11-28z compared to19z11), p=0.63 (4H11z compared to 4H11-28z).

FIGS. 15A-15C: MUC-CD targeted 4H11-28z⁺ T cells successfully traffic toip OV-CAR3(MUC-CD/GFP-FFLuc) tumors following systemic intravenousinfusion resulting in equally efficient anti-tumor efficacy whencompared to ip 4H11-28z⁺ treated tumor bearing mice. FIG. 15A:Kaplan-Meier survival curve of SCID-Beige mice treated ip or iv with4H11-28z⁺ T cells. SCID-Beige mice were injected intraperitoneally with3×10⁶ OV-CAR3(MUC-CD/GFP-FFLuc) tumor cells followed by either iv or ipinfusion of 3×10⁷ 4H11-28z⁺ T cells. Tumor eradication is enhanced aftereither ip or iv infusion of 4H11-28z⁺ T cells when compared to controltreated mice. Both ip and iv 4H11-28z⁺ T cell treated mice exhibitedstatistically enhanced survival (***p<0.0001 and **p=0.0038,respectively) when compared to 19-28z⁺ T cell treated control cohorts.Conversely, difference in survival between the ip and iv 4H11-28z⁺ Tcell cohorts was not statistically significant (p=0.22). FIG. 15B: BLIof tumor progression of representative ip and iv 4H11-28z⁺ T celltreated mice with ultimately progressive disease following treatmentcompared to BLI of tumor progression in a representative control 19-28z⁺T cell treated mouse. FIG. 15C: Systemically injected CFSE stained4H11-28z⁺ T cells traffic to advanced ip OV-CAR(MUC-CD) tumors. Presenceof iv injected CFSE labeled 19-28z⁺ control T cells (left panel) and4H11-28z⁺ T cells (right panel) 1 day following infusion into SCID-Beigemice with advanced OV-CAR(MUC-CD) tumors (injected 7 days earlier), asassessed by FACS analysis of single cell OV-CAR3(MUC-CD) tumorsuspensions, reveals a marked population of 4H11-28z⁺ but not control19-28z⁺ T cells within peritoneal OV-CAR3(MUC-CD) tumors.

FIGS. 16A-16B. Eradication of advanced OV-CAR3(MUC-CD) tumors inSCID-Beige mice by ip infusion of 4H11-28z⁺ T cells. SCID-Beige micewere injected ip with 3×10⁶ OV-CAR3(MUC-CD/GFP-FFLuc) tumor cells 7 daysprior to ip treatment with 3×10⁷ 4H11-28z⁺ T cells. FIG. 16A: BLI of4H11-28z⁺ T cell treated mice with either relapsed disease (middle row)or eradicated disease (bottom row) compared to a representative 19-28z⁺T cell treated control mouse. FIG. 16B: Kaplan-Meier survival curve ofSCID-Beige mice with advanced OV-CAR3(MUC-CD/GFP-FFLuc) tumors treatedip with 4H11-28z⁺ T cells. All 4H11-28z⁺ T cell treated micedemonstrated enhanced survival when compared to control 19-28z⁺ T celltreated mice (**p=0.0011), with an overall long-term survival of 25% atday 120.

FIG. 17: CD8 leader sequence (SEQ ID NO:32), CD3 zeta chainintracellular domain sequence (SEQ ID NO:33), (G4S)3 serine-glycinelinker sequence (SEQ ID NO:34), CD8 transmembrane domain sequence (SEQID NO:35), and CD28 transmembrane+intracellular domains (-STOP) sequence(SEQ ID NO:36).

FIGS. 18A-18E: SFG_4H11z sequence.

FIGS. 19A-19F: SFG-4H11-28z sequence.

FIG. 20: (A) Mouse MUC16-CD Peptide 1 (SEQ ID NO:21), Mouse firstCysteine Loop Peptide 2 (SEQ ID NO:22), and Mouse second Cysteine LoopPeptide 3 (SEQ ID NO:23). (B) Alignment of mouse MUC16 (SEQ ID NO:24)and human MUC16 (SEQ ID NO:25) amino acid sequences. A cysteine wasadded to the peptide sequence at the N terminus of Peptide 1 and Peptide3 for better conjugation with KLH.

FIG. 21: ID8 extract with 1:10 dilution of Mouse MUC16 monoclonalPrimary Supernatants.

FIG. 22: BR5-FVB1 extract with 1:10 dilution of Mouse MUC16 monoclonalPrimary Supernatants

FIG. 23A and FIG. 23B: Western Blot showing 38 hamster's monoclonalantibody Supernatants on ID8 cell extracts.

FIG. 24A: Nucleotide sequence encoding 12B10-3G10-V_(H) (SEQ ID NO:26),FIG. 24B: 12B10-3G10-V_(H) Amino Acid sequence (SEQ ID NO:27), FIG. 24C:Nucleotide sequence encoding 12B10-3G10-V_(L) (SEQ ID NO:28) (Note theV_(L) has an optional NotI site added by the primer for cloning, andFIG. 24D: 12B10-3G10-V_(L) Amino Acid sequence (SEQ ID NO:29).

FIG. 25: FACS Analysis with Purified 12B10-3G10 mAb on ID8 (mouse),OVCAR-3 (human) and BR5-FVB1 (mouse) cell lines.

DEFINITIONS

To facilitate understanding of the invention, a number of terms aredefined below.

The terms “purified,” “isolated,” and grammatical equivalents thereof asused herein, refer to the reduction in the amount of at least oneundesirable component (such as cell, protein, nucleic acid sequence,carbohydrate, etc.) from a sample, including a reduction by anynumerical percentage of from 5% to 100%, such as, but not limited to,from 10% to 100%, from 20% to 100%, from 30% to 100%, from 40% to 100%,from 50% to 100%, from 60% to 100%, from 70% to 100%, from 80% to 100%,and from 90% to 100%. Thus purification results in an “enrichment,”i.e., an increase in the amount of a desirable component cell, protein,nucleic acid sequence, carbohydrate, etc.).

The term “antibody” refers to an immunoglobulin (e.g., IgG, IgM, IgA,IgE, IgD, etc.). The basic functional unit of each antibody is animmunoglobulin (Ig) mononer (containing only one immunoglobulin (“Ig”)unit). Included within this definition are polyclonal antibody,monoclonal antibody, and chimeric antibody.

The variable part of an antibody is its “V domain” (also referred to as“variable region”), and the constant part is its “C domain” (alsoreferred to as “constant region”) such as the kappa, lambda, alpha,gamma, delta, epsilon and mu constant regions. The “variable domain” isalso referred to as the “Fv region” and is the most important region forbinding to antigens. More specifically, variable loops, three each onthe light (V_(L)) and heavy (V_(H)) chains are responsible for bindingto the antigen. These loops are referred to as the “complementaritydetermining regions” (“CDRs” and “idiotypes.”

The immunoglobulin (Ig) monomer of an antibody is a “Y”-shaped moleculethat contains four polypeptide chains: two light chains and two heavychains, joined by disulfide bridges.

Light chains are classified as either (λ) or kappa (κ). A light chainhas two successive domains: one constant domain (“C_(L)”) and onevariable domain (“V_(L)”). The variable domain, V_(L), is different ineach type of antibody and is the active portion of the molecule thatbinds with the specific antigen. The approximate length of a light chainis 211 to 217 amino acids.

Each heavy chain has two regions, the constant region and the variableregion. The There are five types of mammalian Ig heavy denoted a α, δ,ε, γ, and μ. The type of heavy chain present defines the class ofantibody; these chains are found in IgA, IgD, IgE, IgG, and IgMantibodies, respectively. Distinct heavy chains differ in size andcomposition; α and γ contain approximately 450 amino acids, while μ andε have approximately 550 amino acids. Each heavy chain has two regions,the constant region (“C_(H)”) and the variable (“V_(H)”) region. Theconstant region (C_(H)) is identical in all antibodies of the sameisotype, but differs in antibodies of different isotypes. Heavy chainsγ, α and δ have a constant region composed of three tandem (in a line)Ig domains, and a hinge region for added flexibility. Heavy chains μ andε have a constant region composed of four immunoglobulin domains. Thevariable region (V_(H)) of the heavy chain differs in antibodiesproduced by different B cells, but is the same for all antibodiesproduced by a single B cell or B cell clone. The variable region of eachheavy chain is approximately 110 amino acids long.

The term “specifically binds” and “specific binding” when made inreference to the binding of two molecules (e.g. antibody to an antigen,etc.) refer to an interaction of the two molecules that is dependentupon the presence of a particular structure on one or both of themolecules. For example, if an antibody is specific for epitope “A” onthe molecule, then the presence of a protein containing epitope A (orfree, unlabelled A) in a reaction containing labeled “A” and theantibody will reduce the amount of labeled A bound to the antibody.

The term “capable of binding” when made in reference to the interactionbetween a first molecule (such as antibody, polypeptide, glycoprotein,nucleic acid sequence, etc.) and a second molecule (such as antigen,polypeptide, glycoprotein, nucleic acid sequence, etc.) means that thefirst molecule binds to the second molecule in the presence of suitableconcentration of salts, and suitable temperature, and pH. The conditionsfor binding molecules may be determined using routine and/orcommercially available methods

The terms “antigen,” “immunogen,” “antigenic,” “immunogenic,”“antigenically active,” “immunologic,” and “immunologically active” whenmade in reference to a molecule, refer to any substance that is capableof inducing a specific humoral immune response (including eliciting asoluble antibody response) and/or cell-mediated immune response(including eliciting a CTL response). Antigenic peptides preferablycontain at least 5, at least 6, at least 7, at least 8, at least 9, andmore preferably at least 10 amino acids. To elicit antibody production,in one embodiment, antigens may be conjugated to keyhole limpethemocyanin (KLH) or fused to glutathione-S-transferase (GST).

A “cognate antigen” when in reference to an antigen that binds to anantibody, refers to an antigen that is capable of specifically bindingto the antibody.

In one embodiment, the antigen comprises an epitope. The terms “epitope”and “antigenic determinant” refer to a structure on an antigen, whichinteracts with the binding site of an antibody or T cell receptor as aresult of molecular complementarity. An epitope may compete with theintact antigen, from which it is derived, for binding to an antibody.

As used herein the terms “portion” and “fragment” when made in referenceto a nucleic acid sequence or protein sequence refer to a piece of thatsequence that may range in size from 2 contiguous nucleotides and aminoacids, respectively, to the entire sequence minus one nucleotide andamino acid, respectively.

A “subject” that may benefit from the invention's methods includes anymulticellular animal, preferably a mammal. Mammalian subjects includehumans, non-human primates, murines, ovines, bovines, ruminants,lagomorphs, porcines, caprines, equines, canines, felines, aves, etc.).Thus, mammalian subjects are exemplified by mouse, rat, guinea pig,hamster, ferret and chinchilla. The invention's compositions and methodsare also useful for a subject “in need of reducing one or more symptomsof” a disease, e.g., in need of reducing cancer metastasis and/or inneed of reducing one or more symptoms of cancer, includes a subject thatexhibits and/or is at risk of exhibiting one or more symptoms of thedisease. For Example, subjects may be at risk based on family history,genetic factors, environmental factors, etc. This term includes animalmodels of the disease. Thus, administering a composition (which reducesa disease and/or which reduces one or more symptoms of a disease) to asubject in need of reducing the disease and/or of reducing one or moresymptoms of the disease includes prophylactic administration of thecomposition (i.e., before the disease and/or one or more symptoms of thedisease are detectable) and/or therapeutic administration of thecomposition (i.e., after the disease and/or one or more symptoms of thedisease are detectable). The invention's compositions and methods arealso useful for a subject “at risk” for disease (such as cancer) refersto a subject that is predisposed to contracting and/or expressing one ormore symptoms of the disease. This predisposition may be genetic (e.g.,a particular genetic tendency to expressing one or more symptoms of thedisease, such as heritable disorders, etc.), or due to other factors(e.g., environmental conditions, exposures to detrimental compounds,including carcinogens, present in the environment, etc.). The termsubject “at risk” includes subjects “suffering from disease,” i.e., asubject that is experiencing one or more symptoms of the disease. It isnot intended that the present invention be limited to any particularsigns or symptoms. Thus, it is intended that the present inventionencompass subjects that are experiencing any range of disease, fromsub-clinical symptoms to full-blown disease, wherein the subjectexhibits at least one of the indicia (e.g., signs and symptoms)associated with the disease.

“Cancer cell” refers to a cell undergoing early, intermediate oradvanced stages of multi-step neoplastic progression as previouslydescribed (Pitot et al., Fundamentals of Oncology, 15-28 (1978)). Thisincludes cells in early, intermediate and advanced stages of neoplasticprogression including “pre-neoplastic cells (i.e., “hyperplastic cellsand dysplastic cells), and neoplastic cells in advanced stages ofneoplastic progression of a dysplastic cell.

“Metastatic” cancer cell refers to a cancer cell that is translocatedfrom a primary cancer site (i.e., a location where the cancer cellinitially formed from a normal, hyperplastic or dysplastic cell) to asite other than the primary site, where the translocated cancer celllodges and proliferates.

“Cancer” refers to a plurality of cancer cells that may or may not bemetastatic, such as ovarian cancer, breast cancer, lung cancer, prostatecancer, cervical cancer, pancreatic cancer, colon cancer, stomachcancer, esophagus cancer, mouth cancer, tongue cancer, gum cancer, skincancer (e.g., melanoma, basal cell carcinoma, Kaposi's sarcoma, etc.),muscle cancer, heart cancer, liver cancer, bronchial cancer, cartilagecancer, bone cancer, testis cancer, kidney cancer, endometrium cancer,uterus cancer, bladder cancer, bone marrow cancer, lymphoma cancer,spleen cancer, thymus cancer, thyroid cancer, brain cancer, neuroncancer, mesothelioma, gall bladder cancer, ocular cancer (e.g., cancerof the cornea, cancer of uvea, cancer of the choroids, cancer of themacula, vitreous humor cancer, etc.), joint cancer (such as synoviumcancer), glioblastoma, lymphoma, and leukemia.

“Sample” and “specimen” as used herein are used in their broadest senseto include any composition that is obtained and/or derived from abiological source, as well as sampling devices (e.g., swabs), which arebrought into contact with biological or environmental samples.“Biological samples” include those obtained from a subject, includingbody fluids (such as urine, blood, plasma, fecal matter, cerebrospinalfluid (CSF), semen, sputum, and saliva), as well as solid tissue.Biological samples also include a cell (such as cell lines, cellsisolated from tissue whether or not the isolated cells are culturedafter isolation from tissue, fixed cells such as cells fixed forhistological and/or immunohistochemical analysis), tissue (such asbiopsy material), cell extract, tissue extract, and nucleic acid (e.g.,DNA and RNA) isolated from a cell and/or tissue, and the like. Theseexamples are illustrative, and are not to be construed as limiting thesample types applicable to the present invention.

“Overexpression of MUC16” by a cell of interest (such as a cancer cell)refers to a higher level of MUC16 protein and/or mRNA that is expressedby the cell of interest compared to a control cell (such as anon-cancerous cell, normal cell, etc.).

“Internalize” when in reference to a cell refers to entry from theextracellular medium into the cell membrane and/or cytoplasm.

“Glycosylated” when in reference to a sequence (e.g., an amino acidsequence or nucleotide sequence) refers to a sequence that is covalentlylinked to one or more saccharides.

“Pharmaceutical” and “physiologically tolerable” composition refers to acomposition that contains pharmaceutical molecules, i.e., molecules thatare capable of administration to or upon a subject and that do notsubstantially produce an undesirable effect such as, for example,adverse or allergic reactions, dizziness, gastric upset, toxicity andthe like, when administered to a subject. Preferably also, thepharmaceutical molecule does not substantially reduce the activity ofthe invention's compositions. Pharmaceutical molecules include “diluent”(i.e., “carrier”) molecules and excipients.

“Immunogenically effective” and “antigenically effective” amount of amolecule interchangeably refer to an amount of the molecule that iscapable of inducing a specific humoral immune response (includingeliciting a soluble antibody response) and/or cell-mediated immuneresponse (including eliciting a cytotoxic T-lymphocyte (CTL) response).

“Treating” a disease refers to reducing one or more symptoms (such asobjective, subjective, pathological, clinical, sub-clinical, etc.) ofthe disease.

The terms “reduce,” “inhibit,” “diminish,” “suppress,” “decrease,” andgrammatical equivalents (including “lower,” “smaller,” etc.) when inreference to the level of any molecule (e.g., amino acid sequence, andnucleic acid sequence, antibody, etc.), cell, and/or phenomenon (e.g.,disease symptom, binding to a molecule, specificity of binding of twomolecules, affinity of binding of two molecules, specificity to cancer,sensitivity to cancer, affinity of binding, enzyme activity, etc.) in afirst sample (or in a first subject) relative to a second sample (orrelative to a second subject), mean that the quantity of molecule, celland/or phenomenon in the first sample (or in the first subject) is lowerthan in the second sample (or in the second subject) by any amount thatis statistically significant using any art-accepted statistical methodof analysis. In one embodiment, the quantity of molecule, cell and/orphenomenon in the first sample (or in the first subject) is at least 10%lower than, at least 25% lower than, at least 50% lower than, at least75% lower than, and/or at least 90% lower than the quantity of the samemolecule, cell and/or phenomenon in the second sample (or in the secondsubject). In another embodiment, the quantity of molecule, cell, and/orphenomenon in the first sample (or in the first subject) is lower by anynumerical percentage from 5% to 100%, such as, but not limited to, from10% to 100%, from 20% to 100%, from 30% to 100%, from 40% to 100%, from50% to 100%, from 60% to 100%, from 70% to 100%, from 80% to 100%, andfrom 90% to 100% lower than the quantity of the same molecule, celland/or phenomenon in the second sample (or in the second subject). Inone embodiment, the first subject is exemplified by, but not limited to,a subject that has been manipulated using the invention's compositionsand/or methods. In a further embodiment, the second subject isexemplified by, but not limited to, a subject that has not beenmanipulated using the invention's compositions and/or methods. In analternative embodiment, the second subject is exemplified by, but notlimited to, a subject to that has been manipulated, using theinvention's compositions and/or methods, at a different dosage and/orfor a different duration and/or via a different route of administrationcompared to the first subject. In one embodiment, the first and secondsubjects may be the same individual, such as where the effect ofdifferent regimens (e.g., of dosages, duration, route of administration,etc.) of the invention's compositions and/or methods is sought to bedetermined in one individual. In another embodiment, the first andsecond subjects may be different individuals, such as when comparing theeffect of the invention's compositions and/or methods on one individualparticipating in a clinical trial and another individual in a hospital.

The terms “increase,” “elevate,” “raise,” and grammatical equivalents(including “higher,” “greater,” etc.) when in reference to the level ofany molecule (e.g., amino acid sequence, and nucleic acid sequence,antibody, etc.), cell, and/or phenomenon (e.g., disease symptom, bindingto a molecule, specificity of binding of two molecules, affinity ofbinding of two molecules, specificity to cancer, sensitivity to cancer,affinity of binding, enzyme activity, etc.) in a first sample (or in afirst subject) relative to a second sample (or relative to a secondsubject), mean that the quantity of the molecule, cell and/or phenomenonin the first sample (or in the first subject) is higher than in thesecond sample (or in the second subject) by any amount that isstatistically significant using any art-accepted statistical method ofanalysis. In one embodiment, the quantity of the molecule, cell and/orphenomenon in the first sample (or in the first subject) is at least 10%greater than, at least 25% greater than, at least 50% greater than, atleast 75% greater than, and/or at least 90% greater than the quantity ofthe same molecule, cell and/or phenomenon in the second sample (or inthe second subject). This includes, without limitation, a quantity ofmolecule, cell, and/or phenomenon in the first sample (or in the firstsubject) that is at least 10% greater than, at least 15% greater than,at least 20% greater than, at least 25% greater than, at least 30%greater than, at least 35% greater than, at least 40% greater than, atleast 45% greater than, at least 50% greater than, at least 55% greaterthan, at least 60% greater than, at least 65% greater than, at least 70%greater than, at least 75% greater than, at least 80% greater than, atleast 85% greater than, at least 90% greater than, and/or at least 95%greater than the quantity of the same molecule, cell and/or phenomenonin the second sample (or in the second subject). In one embodiment, thefirst subject is exemplified by, but not limited to, a subject that hasbeen manipulated using the invention's compositions and/or methods. In afurther embodiment, the second subject is exemplified by, but notlimited to, a subject that has not been manipulated using theinvention's compositions and/or methods. In an alternative embodiment,the second subject is exemplified by, but not limited to, a subject tothat has been manipulated, using the invention's compositions and/ormethods, at a different dosage and/or for a different duration and/orvia a different route of administration compared to the first subject.In one embodiment, the first and second subjects may be the sameindividual, such as where the effect of different regimens (e.g., ofdosages, duration, route of administration, etc.) of the invention'scompositions and/or methods is sought to be determined in oneindividual. In another embodiment, the first and second subjects may bedifferent individuals, such as when comparing the effect of theinvention's compositions and/or methods on one individual participatingin a clinical trial and another individual in a hospital.

The terms “alter” and “modify” when in reference to the level of anymolecule and/or phenomenon refer to an increase or decrease.

Reference herein to any numerical range expressly includes eachnumerical value (including fractional numbers and whole numbers)encompassed by that range. To illustrate, and without limitation,reference herein to a range of “at least 50” includes whole numbers of50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, etc., and fractional numbers50.1, 50.2 50.3, 50.4, 50.5, 50.6, 50.7, 50.8, 50.9, etc. In a furtherillustration, reference herein to a range of “less than 50” includeswhole numbers 49, 48, 47, 46, 45, 44, 43, 42, 41, 40, etc., andfractional numbers 49.9, 49.8, 49.7, 49.6, 49.5, 49.4, 49.3, 49.2, 49.1,49.0, etc. In yet another illustration, reference herein to a range offrom “5 to 10” includes each whole number of 5, 6, 7, 8, 9, and 10, andeach fractional number such as 5.1, 5.2, 5.3, 5.4, 5.5, 5.6, 5.7, 5.8,5.9, etc.

DESCRIPTION OF THE INVENTION

The invention provides antibodies, and antigen-binding fragmentsthereof, that specifically bind to a polypeptide, or antigenic portionthereof, wherein the polypeptide is selected from a) MUC16 ectodomainpolypeptide, b) MUC16 cytoplasmic domain polypeptide, and c) MUC16extracellular domain polypeptide that contains a cysteine looppolypeptide. The invention's antibodies and compositions containing themare useful in diagnostic and therapeutic applications for diseases inwhich MUC16 is overexpressed, such as cancer.

Using synthetic peptides, the inventors raised novel-specific antibodiesto the carboxy-terminal portion of MUC16, retained by the cell, proximalto the putative cleavage site. These antibodies were characterized usingfluorescence-activated cell-sorting analysis, enzyme-linked immunoassay,Western blot analysis, and immunohistochemistry. Each of the selectedmonoclonal antibodies was reactive against recombinant GST-ΔMUC16^(c114)protein and the MUC16 transfected SKOV3 cell line. Three antibodies,4H11, 9C9, and 4A5 antibodies demonstrated high affinities by Westernblot analysis and saturation-binding studies of transfected SKOV3 cells,and displayed antibody internalization. Immunohistochemical positivitywith novel antibody 4H11 was similar to OC125, but with importantdifferences, including diffuse positivity in lobular breast cancer and asmall percentage of OC125-negative ovarian carcinomas which showedintense and diffuse 4H11 antibody binding.

The invention's compositions and methods are useful for diagnostic andtherapeutic applications, as well as biologic studies such as membranereceptor trafficking and intracellular events. Diagnostic applicationsinclude, for example, detection of cancer using immunohistochemical,radiographic imaging, enzyme-linked immunosorbent assay (ELISA),fluorescence-activated cell sorting (FACS), Western blot, and/orimmunoprecipitation detection.

The invention is further described under (A) MUC16, (B) Prior ArtAntibodies, (C) Invention's Antibodies, (D) Hybridoma Cell Lines, (E)Conjugates Of The Invention's Antibodies Linked To Cytotoxic AgentsAnd/Or Prodrugs, (F) Detecting Muc16 Portions And DiagnosticApplications, and (G) Therapeutic Applications.

A. MUC16

“MUC16,” “MUC-16” and “Mucin 16” interchangeably refer to a type Imembrane protein that is part of a family of tethered mucins. Aschematic of Muc16 is in FIG. 10, and an exemplary human Muc16 aminoacid sequence (SEQ ID NO: 13) is shown in FIGS. 9A-9F. An alignment ofmouse MUC16 (SEQ ID NO:24) and human MUC16 (SEQ ID NO:25) amino acidsequences is shown in FIG. 20B. The term “type 1 protein” refers to a“membrane protein” that is at least partially embedded in the lipidbilayer of a cell, virus and the like, and that contains a transmembranedomain (TM) sequence embedded in the lipid bilayer of the cell, virusand the like. The portion of the protein on the NH₂-terminal side of theTM domain is exposed on the exterior side of the membrane, and theCOOH-terminal portion is exposed on the cytoplasmic side.

Recently, the sequence of the cDNA-encoding MUC16/CA125 was described byYin and Lloyd in 2001 and completed by O'Brien in 2002 (10-12). Thecomplete MUC16 protein has various components consisting of acytoplasmic tail with potential phosphorylation sites, a transmembranedomain, and an external domain proximal to an apparent cleavage site.Distal to the cleavage site, the released external domain contains 16-20tandem repeats of 156 amino acids, each with many potentialglycosylation sites (11). The overall repeat structure (FIG. 10) is wellconserved across mammals, but the repeats are not completely identicalin exact amino acid composition.

The MUC16 protein is part of a family of tethered mucins that includesboth MUC1 and MUC4 (13). MUC1 is present in a variety of tissues andappears to signal through a beta catenin pathway, interact with EGFreceptor, mediates drug resistance and can act as an oncogene (14-17).The MUC4 protein is also expressed in a variety of tissues but is commonon neoplasms of the gastrointestinal track (18-20). In contrast, theCA125 antigen has been more restricted in its distribution and ispresent primarily in gynecologic tissues and overexpressed in Millerianneoplasms (21). However, the CA125 antigen, recognized by the OC125antibody, is a heavily glycosylated antigen expressed in the tandemrepeat region of the larger MUC16 protein. This glycoprotein istypically shed from a putative cleavage site in the extracellular domainof the MUC16 peptide backbone.

Thus, “MUC16” protein contains (a) a “cytoplasmic domain,” (b) a“transmembrane domain,” and (c) a “extracellular domain.” The MUC16extracellular domain contains a cleavage site between a non-glycosylatedectodomain and a large glycosylated ectodomain of tandem repeats.

The terms “cytoplasmic domain,” “cytoplasmic tail,” and “CT” are usedinterchangeably to refer to a protein sequence, and portions thereof,that is on the cytoplasmic side of the lipid bilayer of a cell, virusand the like. Methods for determining the CT of a protein are known inthe art Elofsson et al. (2007) Annu. Rev. Biochem. 76:125-140; Bernselet al. (2005) Protein Science 14:1723-1728).

The terms “transmembrane domain” and “TM” are used interchangeably torefer to a protein sequence, and portions thereof, that spans the lipidbilayer of a cell, virus and the like. Methods for determining the TM ofa protein are known in the art (Elofsson et al. (2007) Annu. Rev.Biochem. 76:125-140; Bernsel et al. (2005) Protein Science14:1723-1728).

The terms “ectodomain” and “extracellular domain” are interchangeablyused when in reference to a membrane protein to refer to the portion ofthe protein that is exposed on the extracellular side of a lipid bilayerof a cell, virus and the like. Methods for determining the ectodomain ofa protein are known in the art (Singer (1990) Annu. Rev. Cell Biol.6:247-296 and High et al. (1993) J. Cell Biol. 121:743-750, and McVectorsoftware, Oxford Molecular).

The exemplary Muc16 of FIGS. 9A-9F contains (a) a “MUC16 cytoplasmicdomain” from amino acid 14476 to 14507, vttrr rkkegeynvq qqcpgyyqshldledlq (SEQ ID NO:16), that interacts with the intracellular signaltransduction machinery; (b) a “MUC16 transmembrane domain” from aminoacid 14452 to 14475, fwaviligl agllgvitcl icgvl (SEQ ID NO: 14) thatspans the plasma membrane; and (c) a “MUC16 extracellular domain” aminoacid 1 to 14392 (SEQ ID NO: 13) that contains a cleavage site between annon-glycosylated ectodomain and a large glycosylated ectodomain oftandem repeats. The “MUC16 ectodomain” is exemplified by nfsplarrvdrvaiyee flrmtrngtq lqnftldrss vlvdgyspnr nepltgnsdl p (SEQ ID NO: 17)from amino acid 14394 to 14451 of SEQ ID NO:13 of FIGS. 9A-9F.

The exemplary MUC16 ectodomain contains both Polypeptide 1 (nfsplarrvdrvaiyee (SEQ ID NO:01), which is from amino acid 14394 to 14410 ofSEQ ID NO: 13), and Polypeptide 2 (tldrss vlvdgyspnr ne (SEQ ID NO:02),which is from amino acid 14425 to 14442 of SEQ ID NO: 13), against whichthe invention's exemplary antibodies were produced. Polypeptide 3,cgvlvttrr rkkegeynvq qq (SEQ ID NO:03) is from amino acid 14472 to 14492of SEQ ID NO: 13, and contains both a transmembrane domain portion(cgvl) and a cytoplasmic domain portion (vttrr rkkegeynvq qq (SEQ IDNO:18)). Thus, the CGVL is optional in SEQ ID NO:03, as it is part ofthe transmembrane domain.

Polypeptide 4 (ksyf sdcqvstfrs vpnrhhtgvd slcnfspl (SEQ ID NO: 15), islocated in a non-glycosylated portion of the Muc16 extracellular domain,is from amino acid 14367 to 14398 of SEQ ID NO: 13, and contains acysteine loop polypeptide cqvstfrsvpnrhhtgvdslc (SEQ ID NO:13).

B. Prior Art Antibodies

The expression of the MUC16/CA125 antigen has long been associated withgynecologic tissues. “CA125,” “CA-125,” “Cleaved CA125,” and “cleavedCA-125,” interchangeably refer to the glycosylated external domain ofthe tethered mucin MUC16, that is distal to the cleavage site (Payne etal., U.S. Pat. No. 7,202,346). This released external domain contains16-20 tandem repeats of 156 amino acids, each with potentialglycosylation sites. An apparent cysteine-based disulfide loop of 19amino acids is present in all repeats and the N-terminal end contains ahairbrush structure that is heavily O-glycosylated (11). The deducedsize would be 2.5 MD for the protein part, and with added carbohydrates,this could increase to 5 MD (10, 26).

CA125, though it is not sensitive or specific enough to be used as ageneral screening tool, is routinely used to monitor patients withovarian carcinoma. The tests used to measure CA125 are antibody baseddetection methods, as are the immunohistochemical stains routinelyperformed for diagnostic purposes. The epitope specificity of 26antibodies to MUC16 was studied in the first report from theInternational Society of Oncodevelopmental Biology and Medicine (ISOBM)TD-1 Workshop and the application of 22 antibodies toimmunohistochemistry was reported in the second report from the TD-1workshop (7, 21). The existing antibodies were grouped as OC125-like,M11-like, or OV197-like and all of the known antibodies recognized CA125epitopes in the repeating, glycosylated elements in the external domainof the tethered mucin MUC16, distal to the putative cleavage site.

The vast majority of MUC16-reactive antibodies, including OC125, reactwith the glycosylation-dependent antigen present exclusively in thecleaved portion of the molecule so the true distribution of MUC16expression is not known (21). There is currently no antibody availableto track the fate of the remaining MUC16 protein fragment after cleavageand CA125 release.

C. Invention's Antibodies

In order to better explore the biology of human MUC16, the inventorshave derived monoclonal antibodies against the extracellular portion ofthe MUC16-carboxy terminus, proximal to the putative cleavage site, aswell as one monoclonal antibody against the internal cytoplasmic domain.In contrast to prior antibodies, these are derived against the peptidebackbone of MUC16 and are not directed at complex glycoprotein epitopes.Since these epitopes are proximal to the cleavage site, they areunlikely to be found in the circulation and provide novel targets fordiagnostic methods and therapeutic interventions. Data hereindemonstrate the identification and characterization of exemplaryantibodies developed against the MUC16 peptide backbone.

The inventors have developed novel antibodies that are directed at thenon-cleaved, non-glycosylated peptide backbone of MUC16. These areexemplified by both 4H11 and 9C9 antibodies, which react with peptidesequences in the non-cleaved ectodomain of MUC16 and are detectable onthe surface of ovarian cancer cell lines and in paraffin-fixed tissuesfrom human ovarian cancer surgical specimens. The antibodies show highaffinity and are readily internalized by ovarian cancer cells when boundto the ectodomain of MUC16. This suggests that the proximal portion ofMUC16 has an independent biology from the more distal, cleaved portionof the mucin. It also suggests that the proximal portions of MUC16 couldprovide convenient targets for diagnostic and therapeutic interventions.Targeting the peptide backbone of MUC16 provides highly specific tissuedelivery for genetically engineered cells, liposomes, or antibodyconjugates, including conjugates with the invention's antibodies.

The invention's antibodies, exemplified by antibody 4H11, are useful astools in immunohistochemistry. Date herein show that 4H11 is relativelyspecific to high-grade ovarian serous carcinoma. Invasive lobular breastcarcinoma is the major exception and shows extensive MUC16 protein asdetected by 4H11. Lobular carcinoma of the breast has unique biologywhich is characterized by a propensity to metastasize to serosalsurfaces (27). Since MUC16 is the cognate binding partner of mesothelin,this may have important implications for lobular cancer (28). Thediscordance rates for OC125 and 4H11 also suggest that 4H11 mightprovide additional, independent information from OC125 in a subset ofovarian carcinomas. Some tumors that are negative with OC125 retaincytoplasmic and extracellular portions of the MUC16 glycoprotein,portions of the molecule that are likely involved in transduction ofsignals potentially important in the malignant phenotype.

Thus, in one embodiment, the invention provides an isolated antibody, oran antigen-binding fragment thereof, that specifically binds to apolypeptide, or antigenic portion thereof, wherein the polypeptide isexemplified by a) MUC16 ectodomain polypeptide (exemplified by NFSPLARRVDRVAIYEE FLRMTRNGTQ LQNFTLDRSS VLVDGYSPNR NEPLTGNSDL P (SEQ ID NO:17)), b) MUC16 cytoplasmic domain polypeptide (exemplified by VTTRRRKKEGEYNVQ QQ (SEQ ID NO:18), which is contained within each ofCGVLVTTRR RKKEGEYNVQ QQ (SEQ ID NO:03) and LVTTRR RKKEGEYNVQ QQ (SEQ IDNO:20)), and c) MUC16 extracellular domain polypeptide that contains acysteine loop polypeptide CQVSTFRSVPNRHHTGVDSLC (SEQ ID NO: 19).

One advantage of the invention's antibodies is that the antibodyinternalizes into a cell, thereby being useful in applications fordelivery inside a cell, such as disease therapy. “Internalized” when inreference to a molecule that is internalized by a cell refers to passageof the molecule that is in contact with the extracellular surface of acell membrane across the cell membrane to the intracellular surface ofthe cell membrane and/or into the cell cytoplasm. Methods fordetermining internalization are disclosed herein, including thedetection of radiolabeled molecule inside the cell (FIG. 5E).

In one embodiment, the invention's antibodies specifically bind to MUC16ectodomain polypeptide that comprises a polypeptide selected from thegroup consisting of Polypeptide 1 NFSPLARRVDRVAIYEE (SEQ ID NO:01) andPolypeptide 2 TLDRSSVLVDGYSPNRNE (SEQ ID NO:02). Data herein show thatthe invention's antibodies specifically bind to GST-ΔMUC16^(c114)(Example 2, Table 1A). The specificity of the invention's antibodies isin contrast to prior art antibodies (e.g., VK8, M11 and OC125antibodies) that did not bind to GST-ΔMUC16^(c114) purified protein orcell lysates of the SKOV3-phrGFP-ΔMUC16^(c114) cell line (Example 2,FIG. 2).

In a further embodiment, the invention's antibodies lack specificbinding to a glycosylated MUC16 extracellular domain, exemplified by thecleaved CA-125 described in Payne et al., U.S. Pat. No. 7,202,346.

While not intending to limit the sequence of the V_(L) and V_(H) regionsof the invention's antibodies, in one embodiment, the antibodyspecifically binds to the Polypeptide 2 (SEQ ID NO:02) of the MUC16ectodomain polypeptide, wherein the antibody comprises a variable heavy(V_(H)) chain encoded by SEQ ID NO:06 (i.e., the antibody 4H11 variableheavy (V_(H)) chain amino acid sequence of FIG. 8C), and a variablelight (V_(L)) chain encoded by SEQ ID NO:07 (i.e., the antibody 4H11variable light (V_(L)) chain amino acid sequence of FIG. 8D). In aparticular embodiment, the antibody is chimeric, wherein at least one ofthe V_(L) and V_(H) chains is fused to a human immunoglobulin constantregion.

Also without intending to limit the sequence of the V_(L) and V_(H)regions of the invention's antibodies, in one embodiment, the antibodyspecifically binds to the Polypeptide 2 (SEQ ID NO:02) of the MUC16ectodomain polypeptide, wherein the antibody comprises a variable heavy(V_(H)) chain encoded by SEQ ID NO:04 (i.e., the antibody 4A5 variableheavy (V_(H)) chain nucleotide sequence of FIG. 8A), and a variablelight (V_(L)) chain encoded by SEQ ID NO:05 (i.e., the antibody 4A5variable light (V_(L)) chain nucleotide sequence of FIG. 8B). In aparticular embodiment, the antibody is chimeric wherein at least one ofthe V_(L) and V_(H) chains is covalently linked to a humanimmunoglobulin constant region.

Still without intending to limit the sequence of the V_(L) and V_(H)regions of the invention's antibodies, in one embodiment, the antibodyspecifically binds to the Polypeptide 1 (SEQ ID NO:01) of the MUC16ectodomain polypeptide, wherein the antibody comprises a variable heavy(V_(H)) chain encoded by SEQ ID NO:08 (i.e., the antibody 9B11 variableheavy (V_(H)) chain nucleotide sequence of FIG. 8E), and a variablelight (V_(L)) chain encoded by at least one of SEQ ID NO:09 (i.e.,antibody 9B11 variable light (V_(L.A)) chain nucleotide sequence of FIG.8F), and SEQ ID NO: 10 (i.e., the antibody 9B11 variable light (V_(L.B))chain nucleotide sequence of FIG. 8G). In a particular embodiment, theantibody is chimeric wherein at least one of the V_(L) and V_(H) chainsis covalently linked to a human immunoglobulin constant region.

While not intending to restrict the source of antigen to which theinvention's antibodies bind, in one embodiment, the MUC16 ectodomainpolypeptide is expressed by a cell. Data herein show that theinvention's exemplary antibodies bind to SKOV3 cells transduced withphrGFP-ΔMUC16^(c114) (Example 2).

While not limiting the sequence of antigen to which the invention'santibodies bind, in a further embodiment, the invention's antibodiesspecifically bind to a MUC16 cytoplasmic domain polypeptide thatcomprises VTTRR RKKEGEYNVQ QQ (SEQ ID NO: 18). In a particularembodiment, the MUC16 cytoplasmic domain polypeptide comprisesPolypeptide 3 CGVLVTTRRRKKEGEYNVQQQ (SEQ ID NO:03). In some embodiment,the MUC16 cytoplasmic domain polypeptide is expressed by a cell. Forexample, data herein show that the invention's exemplary antibody bindsto SKOV3 cells transduced with phrGFP-ΔMUC16^(c114) (Example 2). In aparticular embodiment, the cell is permeabilized to facilitateinternalization of the antibody into the cell so that it comes intocontact with its cytoplasmic antigen.

Still without limiting the sequence of antigen to which the invention'santibodies bind, in a further embodiment, the invention's antibodiesbind to a MUC16 extracellular domain polypeptide that contains acysteine loop polypeptide CQVSTFRSVPNRHHTGVDSLC (SEQ ID NO:19). In amore preferred embodiment, the MUC16 extracellular domain polypeptidecomprises Polypeptide 4 KSYF SDCQVSTFRS VPNRHHTGVD SLCNFSPL (SEQ IDNO:15).

Still without intending to limit the sequence of the V_(L) and V_(H)regions of the invention's antibodies, in one embodiment, the antibodyspecifically binds to Polypeptide 4 (SEQ ID NO:15) of the MUC16extracellular domain polypeptide, wherein the antibody comprises avariable heavy (V_(H)) chain encoded by SEQ ID NO: 11 (i.e., theantibody 24B3 variable heavy (V_(H)) chain amino acid sequence of FIG.8H), and a variable light (V_(L)) chain encoded by SEQ ID NO: 12 (i.e.,the antibody 24B3 variable light (V_(L)) chain amino acid sequence ofFIG. 8I).

The invention contemplates chimeric antibodies (see U.S. Pat. No.7,662,387), monoclonal antibodies, recombinant antibodies, anantigen-binding fragment of a recombinant antibody, a humanizedantibody, and an antibody displayed upon the surface of a phage (U.S.Pat. No. 7,202,346). In particular, the invention contemplates antibodyfragments that contain the idiotype (“antigen-binding region” or“antigen-binding fragment”) of the antibody molecule. For example, suchantigen-binding fragments include, but are not limited to, the Fabregion, F(ab′)2 fragment, pFc′ fragment, and Fab′ fragments.

The “Fab region” and “fragment, antigen binding region,” interchangeablyrefer to portion of the antibody arms of the immnoglobulin “Y” thatfunction in binding antigen. The Fab region is composed of one constantand one variable domain from each heavy and light chain of the antibody.Methods are known in the art for the construction of Fab expressionlibraries (Huse et al., Science, 246:1275-1281 (1989)) to allow rapidand easy identification of monoclonal Fab fragments with the desiredspecificity. In another embodiment, Fc and Fab fragments can begenerated by using the enzyme papain to cleave an immunoglobulin monomerinto two Fab fragments and an Fc fragment. The enzyme pepsin cleavesbelow the hinge region, so a “F(ab′)2 fragment” and a “pFc′ fragment” isformed. The F(ab′)2 fragment can be split into two “Fab′ fragments” bymild reduction.

The invention also contemplates a “single-chain antibody” fragment,i.e., an amino acid sequence having at least one of the variable orcomplementarity determining regions (CDRs) of the whole antibody, andlacking some or all of the constant domains of the antibody. Theseconstant domains are not necessary for antigen binding, but constitute amajor portion of the structure of whole antibodies. Single-chainantibody fragments are smaller than whole antibodies and may thereforehave greater capillary permeability than whole antibodies, allowingsingle-chain antibody fragments to localize and bind to targetantigen-binding sites more efficiently. Also, antibody fragments can beproduced on a relatively large scale in prokaryotic cells, thusfacilitating their production. Furthermore, the relatively small size ofsingle-chain antibody fragments makes them less likely to provoke animmune response in a recipient than whole antibodies. Techniques for theproduction of single-chain antibodies are known (U.S. Pat. No.4,946,778). The variable regions of the heavy and light chains can befused together to form a “single-chain variable fragment” (“scFvfragment”), which is only half the size of the Fab fragment, yet retainsthe original specificity of the parent immunoglobulin.

The “Fc region” and “Fragment, crystallizable region” interchangeablyrefer to portion of the base of the immnoglobulin “Y” that function inrole in modulating immune cell activity. The Fc region is composed oftwo heavy chains that contribute two or three constant domains dependingon the class of the antibody. By binding to specific proteins, the Fcregion ensures that each antibody generates an appropriate immuneresponse for a given antigen. The Fc region also binds to various cellreceptors, such as Fc receptors, and other immune molecules, such ascomplement proteins. By doing this, it mediates different physiologicaleffects including opsonization, cell lysis, and degranulation of mastcells, basophils and eosinophils. In an experimental setting, Fc and Fabfragments can be generated in the laboratory by cleaving animmunoglobulin monomer with the enzyme papain into two Fab fragments andan Fc fragment.

The invention contemplates polyclonal antibodies and monoclonalantibodies. “Polyclonal antibody” refers to an immunoglobulin producedfrom more than a single clone of plasma cells; in contrast “monoclonalantibody” refers to an immunoglobulin produced from a single clone ofplasma cells. Generic methods are available for making polyclonal andmonoclonal antibodies that are specific to a desirable polypeptide. Forthe production of monoclonal and polyclonal antibodies, various hostanimals can be immunized by injection with the peptide corresponding toany molecule of interest in the present invention, including but notlimited to hamsters, rabbits, mice, rats, sheep, goats, etc. Forpreparation of monoclonal antibodies, any technique that provides forthe production of antibody molecules by continuous cell lines in culturemay be used (See e.g., Harlow and Lane, Antibodies: A Laboratory Manual,Cold Spring Harbor Laboratory Press, Cold Spring Harbor, N.Y.). Theseinclude, but are not limited to, the hybridoma technique originallydeveloped by Kohler and Milstein (Kohler and Milstein, Nature,256:495-497 (1975)), techniques using germ-free animals and utilizingtechnology such as that described in PCT/US90/02545, as well as thetrioma technique, the human B-cell hybridoma technique (See e.g., Kozboret al., Immunol. Today, 4:72 (1983)), and the EBV-hybridoma technique toproduce human monoclonal antibodies (Cole et al., in MonoclonalAntibodies and Cancer Therapy, Alan R. Liss, Inc., pp. 77-96 (1985)). Insome particularly preferred embodiments of the present invention, thepresent invention provides monoclonal antibodies.

Also contemplated are chimeric antibodies. As used herein, the term“chimeric antibody” contains portions of two different antibodies,typically of two different species. See, e.g.: U.S. Pat. No. 4,816,567to Cabilly et al.; U.S. Pat. No. 4,978,745 to Shoemaker et al.; U.S.Pat. No. 4,975,369 to Beavers et al.; and U.S. Pat. No. 4,816,397 toBoss et al. Chimeric antibodies include monovalent, divalent orpolyvalent immunoglobulins. A monovalent chimeric antibody is a dimer(HL) formed by a chimeric H chain associated through disulfide bridgeswith a chimeric L chain. A divalent chimeric antibody is tetramer (H₂L₂)formed by two HL dimers associated through at least one disulfidebridge. A polyvalent chimeric antibody can also be produced, forexample, by employing a He region that aggregates (e.g., IgM H chain).

The invention also contemplates “humanized antibodies,” i.e., chimericantibodies that have constant regions derived substantially orexclusively from human antibody constant regions, and variable regionsderived substantially or exclusively from the sequence of the variableregion from a mammal other than a human. Humanized antibodies preferablyhave constant regions and variable regions other than the complementdetermining regions (CDRs) derived substantially or exclusively from thecorresponding human antibody regions and CDRs derived substantially orexclusively from a mammal other than a human. Thus, in one embodiment,humanized antibodies are human immunoglobulins (recipient antibody) inwhich residues from a hypervariable region of the recipient are replacedby residues from a hypervariable region of a non-human species (donorantibody) such as mouse, rat, rabbit or nonhuman primate having thedesired specificity, affinity, and capacity. In some instances, Fvframework region (FR) residues of the human immunoglobulin are replacedby corresponding non-human residues. Furthermore, humanized antibodiesmay comprise residues that are not found in the recipient antibody or inthe donor antibody. These modifications are generally made to furtherrefine antibody performance. In general, the humanized antibody willcomprise substantially all of at least one, and typically two, variabledomains, in which all or substantially all of the hypervariable loopscorrespond to those of a nonhuman immunoglobulin and all orsubstantially all of the FR residues are those of a human immunoglobulinsequence. The humanized antibody may also comprise at least a portion ofan immunoglobulin constant region (Fc), typically that of a humanimmunoglobulin. Humanized antibodies may be generated using methodsknown in the art, e.g., U.S. Pat. No. 5,225,539 to Winter et al.,including using human hybridomas (Cote et al., Proc. Natl. Acad. Sci.U.S.A. 80:2026-2030 (1983)) or by transforming human B cells with EBVvirus in vitro (Cole et al., in Monoclonal Antibodies and CancerTherapy, Alan R. Liss, pp. 77-96 (1985)). Additional methods include,for example, generation of transgenic non-human animals which containhuman immunoglobulin chain genes and which are capable of expressingthese genes to produce a repertoire of antibodies of various isotypesencoded by the human immunoglobulin genes (U.S. Pat. Nos. 5,545,806;5,569,825 and 5,625,126). Humanized antibodies may also be made bysubstituting the complementarity determining regions of, for example, amouse antibody, into a human framework domain (PCT Pub. No. WO92/22653).

Importantly, early methods for humanizing antibodies often resulted inantibodies with lower affinity than the non-human antibody startingmaterial. More recent approaches to humanizing antibodies address thisproblem by making changes to the CDRs. See U.S. Patent ApplicationPublication No. 20040162413, hereby incorporated by reference. In someembodiments, the invention's humanized antibodies contain an optimizedheteromeric variable region (e.g. that may or may not be part of a fullantibody other molecule) having equal or higher antigen binding affinitythan a donor heteromeric variable region, wherein the donor heteromericvariable region comprises three light chain donor CDRs, and wherein theoptimized heteromeric variable region comprises: a) a light chainaltered variable region comprising; i) four unvaried human germlinelight chain framework regions, and ii) three light chain alteredvariable region CDRs, wherein at least one of the three light chainaltered variable region CDRs is a light chain donor CDR variant, andwherein the light chain donor CDR variant comprises a different aminoacid at only one, two, three or four positions compared to one of thethree light chain donor CDRs (e.g. the at least one light chain donorCDR variant is identical to one of the light chain donor CDRs except forone, two, three or four amino acid differences).

Chimeric antibodies containing amino acid sequences that are fused toconstant regions from human antibodies, or to toxins or to moleculeswith cytotoxic effect, are known in the art (e.g., U.S. Pat. Nos.7,585,952; 7,227,002; 7,632,925; 7,501,123; 7,202,346; 6,333,410;5,475,092; 5,585,499; 5,846,545; 7,202,346; 6,340,701; 6,372,738;7,202,346; 5,846,545; 5,585,499; 5,475,092; 7,202,346; 7,662,387;6,429,295; 7,666,425; and 5,057,313).

Antibodies that are specific for a particular antigen may be screenedusing methods known in the art (e.g., U.S. Pat. No. 7,202,346) anddisclosed herein. For example, In the production of antibodies,screening for the desired antibody can be accomplished byradioimmunoassay, ELISA (enzyme-linked immunosorbent assay), “sandwich”immunoassays, immunoradiometric assays, gel diffusion precipitinreactions, immunodiffusion assays, in situ immunoassays (e.g., usingcolloidal gold, enzyme or radioisotope labels), Western blots,precipitation reactions, agglutination assays (e.g., gel agglutinationassays, hemagglutination assays, etc.), complement fixation assays,immunofluorescence assays, protein A assays, and immunoelectrophoresisassays, etc.

In one embodiment, antibody binding is detected by detecting a label onthe primary antibody. In another embodiment, the primary antibody isdetected by detecting binding of a secondary antibody or reagent to theprimary antibody. In a further embodiment, the secondary antibody islabeled. Many means are known in the art for detecting binding in animmunoassay and are within the scope of the present invention. As iswell known in the art, the immunogenic peptide should be provided freeof the carrier molecule used in any immunization protocol. For example,if the peptide was conjugated to KLH, it may be conjugated to BSA, orused directly, in a screening assay.

In one embodiment, the invention's antibodies are monoclonal antibodiesproduced by a hybridoma cell line. In a particular embodiment, themonoclonal antibody specifically binds to a MUC16 ectodomain polypeptidethat comprises Polypeptide 1 (SEQ ID NO:01), as exemplified by theantibody selected from the group consisting of 9B11.20.16, 10A2, 2F4,23D3, 30B1, and 31B2 (Tables 1 and 2). In a preferred embodiment, theantibody is 9B11.

In another embodiment, the monoclonal antibody specifically binds to aMUC16 ectodomain polypeptide that comprises Polypeptide 2 (SEQ IDNO:02), wherein the antibody is exemplified by 4H11.2.5, 13H1, 29G9,9C9.21.5.13, 28F8, 23G12, 9C7.6, 11B6, 25G4, 5C2.17, 4C7, 26B2, 4A5.37,4A2, 25H3, and 28F7.18.10 (Tables 1 and 2). In a preferred embodiment,the antibody is exemplified by 4H11.2.5, 4A5.37, 9C9.21.5.13,28F7.18.10, 9C7.6, and 5C2.17.

In a further embodiment, the monoclonal antibody specifically binds to aMUC16 cytoplasmic domain polypeptide that comprises Polypeptide 3CGVLVTTRRRKKEGEYNVQQQ (SEQ ID NO:03), wherein the antibody isexemplified by 31A3.5.1, 19D1, 10F6, 22E10, 22F1, 3H8, 22F11, 4D7,24G12, 19G4, 9A5, 4C2, 31C8, 27G4, and 6H2 (Tables 1 and 2). In apreferred embodiment, the antibody is 31A3.5.1.

In another embodiment, the monoclonal antibody specifically binds to aMUC16 extracellular domain polypeptide that comprises Polypeptide 4 KSYFSDCQVSTFRS VPNRHHTGVD SLCNFSPL (SEQ ID NO: 15), wherein the antibody isexemplified by 24B3 and 9C7 (Table 2).

The invention's antibodies and methods for their use (both diagnosticand therapeutic) are disease specific. “Specificity” of a method and/ormolecule for disease, such as “specificity for cancer” which isinterchangeably used with “cancer specificity”, refers to the proportion(e.g., percentage, fraction, etc.) of negatives (i.e., healthyindividuals not having disease) that are correctly identified, i.e., thepercentage of healthy subjects who are correctly identified as nothaving disease. Specificity may be calculated according to the followingequation:Specificity=number of true negatives/(number of true negatives+number offalse positives).Thus, in some embodiments, the invention's compositions and/or methodshave a “cancer specificity” greater than 50%, including any numericalvalue from 51% to 100%, such as 52%, 53%, 54%, 55%, 56%, 57%, 58%, 59%,60%, 61%, 62%, 63%, 64%, 65%, 66%, 67%, 68%, 69%, 70%, 71%, 72%, 73%,74%, 75%, 76%, 77%, 78%, 79%, 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%,88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, and 99%. While a100% specificity is most desirable, i.e., not predicting anyone from thehealthy group as having cancer, it is not necessary. Data hereindemonstrate the invention's cancer specificity (Table 3).

In alternative embodiments, specificity is expressed (together withsensitivity) as a statistical measure of the performance of a binaryclassification test, such as using a Receiver Operator Characteristic(ROC) curve”. For any test, there is usually a trade-off betweenspecificity and sensitivity. For example: in cancer screening tests ofhuman subjects, it is undesirable to risk falsely identifying healthypeople as having cancer (low specificity), due to the high costs. Thesecosts are both physical (unnecessary risky procedures) and financial.This trade-off can be represented graphically using a ROC curve.“Receiver Operator Characteristic curve” and “ROC curve” refer to a plotof the true positive rate (AKA sensitivity) versus true negative rate(AKA 1-specificity). The measured result of the test is represented onthe x axis while the y axis represents the number of control (e.g.,healthy) or case (e.g., cancer) subjects. For any given cut point (eachpoint along the x axis) a sensitivity and specificity of the assay canbe measured. The range of sensitivity and specificity for any givenassay can range from 0% to 100%, depending on the selected cut point.For this reason, in some preferred embodiments, the AUC is used as thestandard measure of an assay's specificity and/or sensitivity. The “areaunder the curve” (“AUC”) for the ROC curve plot is equal to theprobability that a classifier will rank a randomly chosen positiveinstance higher than a randomly chosen negative one. Thus, AUC is ageneral measure of a tests ability to successfully discriminate betweencase (e.g., cancer) and control (e.g., healthy) subjects. Random chancewould generate an AUC of 0.5. Therefore, in one embodiment, useful testspreferably have AUC's greater than 0.50, including any value from 0.51to 1.00, such as from 0.55 to 1.00, from 0.60 to 1.00, from 0.65 to1.00, from 0.70 to 1.00, from 0.75 to 1.00, from 0.80 to 1.00, from 0.85to 1.00, from 0.90 to 1.00, from 0.95 to 1.00, and most preferably 1.00.AUC values greater than 0.50 include 0.51, 0.52, 0.52, 0.54, 0.55, 0.56,0.57, 0.58, 0.59, 0.60, 0.61, 0.62, 0.63, 0.64, 0. 65, 0.66, 0.67, 0.68, 0.69, 0.70, 0.71, 0.72, 0.73, 0.74, 0.75, 0.76, 0.77, 0.78, 0.79,0.80, 0.81, 0.82, 0.83, 0.84, 0.85, 0.86, 0.87, 0.88, 0.89, 0.90, 0.91,0.92, 0.93, 0.94, 0.95, 0.96, 0.97, 0.98, and 0. 99.

The invention's antibodies and methods for their use (both diagnosticand therapeutic) are disease sensitive. “Sensitivity” of a method and/ormolecule for disease, such as “sensitivity for cancer” which isinterchangeably used with “cancer sensitivity,” refers to the proportion(e.g., percentage, fraction, etc.) of positives (i.e., individualshaving cancer) that are correctly identified as such (e.g. thepercentage of people with cancer who are identified as having thecondition). Sensitivity may be calculated according to the followingequation; Sensitivity=number of true positives/(number of truepositives+number of false negatives).

Thus, in some embodiments, the invention's compositions and/or methodshave a “disease sensitivity,” such as “cancer sensitivity,” greater than50%, including any numerical value from 51% to 100%, such as 52%, 53%,54%, 55%, 56%, 57%, 58%, 59%, 60%, 61%, 62%, 63%, 64%, 65%, 66%, 67%,68%, 69%, 70%, 71%, 72%, 73%, 74%, 75%, 76%, 77%, 78%, 79%, 80%, 81%,82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%,96%, 97%, 98%, and 99%. While a 100% sensitivity is most desirable(i.e., predicting all subjects from the cancer group as having cancer),it is not necessary.

In alternative embodiments, the invention's compositions and/or methodshave a “disease sensitivity,” such as “cancer sensitivity,” equal to orlower than 50%, including any numerical value from 0% to 50%, such as1%, 2%, 3%, 4%, 6%, 6%, 7%, 8%, 9%, 10%, 11%, 12%, 13%, 14%, 15%, 16%,17%, 18%, 19%, 20%, 21%, 22%, 23%, 24%, 25%, 26%, 27%, 28%, 29%, 30%,31%, 32%, 33%, 34%, 35%, 36%, 37%, 38%, 39%, 40%, 41%, 42%, 43%, 44%,45%, 46%, 47%, 48%, and 49%.

In some embodiments, sensitivity is expressed (together withspecificity) as a statistical measure of the performance of a binaryclassification test, such as using AUC of a ROC curve, as discussedabove with respect to specificity.

D. Hybridoma Cell Lines

In addition to the invention's novel antibodies, the invention alsoprovides hybridoma cell lines that produce these antibodies. “Hybridomacell” refers to a cell line produced by fusing a specificantibody-producing B cell with a myeloma (B cell cancer) cell that isselected for its ability to grow in tissue culture and for an absence ofantibody chain synthesis. The antibodies produced by the hybridoma cellare all of a single specificity and are therefore monoclonal antibodies(in contrast to polyclonal antibodies).

In a particular embodiment, the invention provides hybridoma cell linesthat produce a monoclonal antibody that specifically binds to apolypeptide, or antigenic portion thereof, selected from the groupconsisting of a) MUC16 ectodomain polypeptide (e.g., NFSPLAR RVDRVAIYEEFLRMTRNGTQ LQNFTLDRSS VLVDGYSPNR NEPLTGNSDL P (SEQ ID NO: 17)), b) MUC16cytoplasmic domain polypeptide (e.g., VTTRR RKKEGEYNVQ QQ (SEQ IDNO:18)), and c) MUC16 extracellular domain polypeptide that contains acysteine loop polypeptide CQVSTFRSVPNRHHTGVDSLC (SEQ ID NO:19). TheMUC16 polypeptide SEQ ID NO: 18 is contained within LVTTRR RKKEGEYNVQ QQ(SEQ ID NO:20). Thus, SEQ ID NO:20 contains both a transmembrane domainamino acid (L) and a cytoplasmic domain portion VTTRR RKKEGEYNVQ QQ (SEQID NO:18), i.e., the L is optional, as it is part of the transmembranedomain. The MUC16 polypeptide SEQ ID NO:18 is also contained withinCGVLVTTRR RKKEGEYNVQ QQ (SEQ ID NO:03). Thus, SEQ ID NO:03 contains botha transmembrane domain portion (CGVL) and a cytoplasmic domain portionVTTRR RKKEGEYNVQ QQ (SEQ ID NO:18), i.e., the CGVL is optional, as it ispart of the transmembrane domain.

E. Conjugates of the Invention's Antibodies Linked to Cytotoxic Agentsand/or Prodrugs

The invention contemplates conjugate antibodies. A “conjugate” antibodyrefers to an antibody of the present invention covalently linked to acytotoxic agent and/or a prodrug of a cytotoxic agent.

“Cytotoxic agent” refers any agent that is capable of reducing thegrowth of, and/or killing, a target cell. A “prodrug” represents ananalog of a cytotoxic agent that substantially lacks cytotoxic activityuntil subjected to an activation step. Activation steps may includeenzymatic cleavage, a chemical activation step such as exposure to areductant, or a physical activation step such as photolysis.

The covalent linkage between the invention's antibodies and thecytotoxic agent or prodrug can include cleavable linkages such asdisulfide bonds, which may advantageously result in cleavage of thecovalent linkage within the reducing environment of the target cell.Such conjugates are useful as tumor-cell specific therapeutic agents.

In one embodiment, the cytotoxic agent is a small drug molecule (Payneet al., U.S. Pat. No. 7,202,346). In another embodiment, the cytotoxicagent a maytansinoid, an analog of a maytansinoid, a prodrug of amaytansinoid, or a prodrug of an analog of a maytansinoid (U.S. Pat.Nos. 6,333,410; 5,475,092; 5,585,499; 5,846,545; 7,202,346). In anotherembodiment, the cytotoxic agent may be a taxane (see U.S. Pat. Nos.6,340,701 & 6,372,738 & 7,202,346) or CC-1065 analog (see U.S. Pat. Nos.5,846,545; 5,585,499; 5,475,092 & 7,202,346).

In another embodiment, the cytotoxic agent is exemplified by anauristatin, a DNA minor groove binding agent, a DNA minor groovealkylating agent, an enediyne, a duocarmycin, a maytansinoid, and avinca alkaloid (U.S. Pat. No. 7,662,387).

In a further embodiment, the cytotoxic agent is an anti-tubulin agent(U.S. Pat. No. 7,662,387). In yet another embodiment, the cytotoxicagent is exemplified bydimethylvaline-valine-dolaisoleuine-dolaproine-phenylalanine-p-phenylenediamine(AFP), dovaline-valine-dolaisoleunine-dolaproine-phenylalanine (MMAF),and monomethyl auristatin E (MAE) (U.S. Pat. No. 7,662,387).

In an additional embodiment the toxic agent is exemplified byradioisotope emitting radiation, immunomodulator, lectin, and toxin(U.S. Pat. No. 6,429,295). In particular, the radioisotope emittingradiation is an alpha-emitter selected from the group consisting of²¹²Bi, ²¹³Bi, and ²¹¹At, or a beta-emitter selected from the groupconsisting of ¹⁸⁶Re and ⁹⁰Y, or a gamma-emitter ¹³¹I (U.S. Pat. No.7,666,425).

In an alternative embodiment, the toxin is exemplified by ricin, theA-chain of ricin, and pokeweed antiviral protein (U.S. Pat. No.5,057,313).

In yet another embodiment, the cytotoxic agent is an anti-cancer drugselected from the group consisting of methotrexate, 5-fluorouracil,cycloheximide, daunomycin, doxorubicin, chlorambucil, trenimon,phenylenediamine mustard, adriamycin, bleomycin, cytosine arabinoside orCyclophosphamide (U.S. Pat. No. 5,057,13).

F. Detecting Muc16 Portions and Diagnostic Applications

The invention provides a method for detecting a disease that comprisesoverexpression of MUC16 in a subject, wherein the method comprises a)providing i) a sample from a subject, and ii) any one or more of theinvention's antibodies, b) contacting the sample with the antibody underconditions for specific binding of the antibody with its cognateantigen, and c) detecting an increased level of binding of the antibodyto the sample compared to a control sample lacking the disease, therebydetecting the disease in the subject. Generic methods for detectingdisease using antibodies are known in the art (Payne et al., U.S. Pat.No. 7,202,346). The invention's methods are particularly useful indetecting cancer, such as ovarian cancer and breast cancer.

The invention's methods are not limited to a particular approach todetecting binding of the invention's antibodies to their antigens. Inone embodiment, detecting binding to the invention's antibodiestypically involves using antibodies that are labeled with a detectablemoiety, such as radioisotope (e.g., ³H, ¹⁴C, ³²P, ³⁵S, and/or ¹²⁵I),fluorescent or chemiluminescent compound (e.g., fluoresceinisothiocyanate, rhodamine, and/or luciferin) and/or an enzyme (e.g.,alkaline phosphatase, beta-galactosidase and/or horseradish peroxidase).

Methods for conjugating antibodies to a detectable moiety are known inthe art (e.g., Hunter, et al., Nature 144:945 (1962); David, e at.,Biochemistry 13:1014 (1974); Pain, et al., J. Immunol. Meth. 40:219(1981); and Nygren, J. Histochem. and Cytochem. 30:407 (1982).

Thus, the invention's antibodies may be employed in immunoassays, suchas competitive binding assays, direct and indirect sandwich assays, andimmunoprecipitation assays, including immunohistochemistry,enzyme-linked immunosorbent assay (ELISA), fluorescence-activated cellsorting (FACS), and Western blots.

For example, with respect to immunohistochemical detection, data hereindemonstrate that antibody 4H11 is useful in detecting high-grade ovarianserous carcinoma, lobular cancer (28), and a subset of ovariancarcinomas that are negative with OC125 and that retain cytoplasmic andextracellular portions of the MUC16 glycoprotein.

The antibodies of the invention also are useful for radiographic in vivoimaging, wherein an antibody labeled with a detectable moiety such as aradio-opaque agent or radioisotope is administered to a subject,preferably into the bloodstream, and the presence and location of thelabeled antibody in the host is assayed. This imaging technique isuseful in the staging and treatment of malignancies.

The invention's antibodies are additionally useful as affinitypurification agents. In this process, the antibodies are immobilized ona suitable support, such a Sephadex resin or filter paper, using methodswell known in the art, to capture and purify molecules that containantigens that specifically bind to the invention's antibodies.

G. Therapeutic Applications

The invention provides methods for treating a disease that comprisesoverexpression of MUC16, comprising administering to a subject havingthe disease a therapeutically effective amount of any one or more of theinvention's antibodies. Generic methods for treating disease withantibodies are known in the art (Payne et al., U.S. Pat. No. 7,202,346).The invention's methods are particularly useful in treating cancer, suchas ovarian cancer and breast cancer. These methods are also applicableto primary cancer, metastatic cancer, and recurrent cancer.

The term “administering” to a subject means providing a molecule to asubject. This may be done using methods known in the art (e.g., Ericksonet al., U.S. Pat. No. 6,632,979; Furuta et al., U.S. Pat. No. 6,905,839;Jackobsen et al., U.S. Pat. No. 6,238,878; Simon et al., U.S. Pat. No.5,851,789). The invention's compositions may be administeredprophylactically (i.e., before the observation of disease symptoms)and/or therapeutically (i.e., after the observation of diseasesymptoms). Administration also may be concomitant with (i.e., at thesame time as, or during) manifestation of one or more disease symptoms.Also, the invention's compositions may be administered before,concomitantly with, and/or after administration of another type of drugor therapeutic procedure (e.g., surgery). Methods of administering theinvention's compositions include, without limitation, administration inparenteral, oral, intraperitoneal, intranasal, topical and sublingualforms. Parenteral routes of administration include, for example,subcutaneous, intravenous, intramuscular, intrastemal injection, andinfusion routes.

In one embodiment, the invention's compositions comprise a lipid fordelivery as liposomes. Methods for generating such compositions areknown in the art (Borghouts et al. (2005). J Pept Sci 11, 713-726; Changet al. (2009) PLoS One 4, e4171; Faisal et al. (2009) Vaccine 27,6537-6545; Huwyler et al. (2008) Int J Nanomedicine 3, 21-29; Song etal. (2008) Int J Pharm 363, 155-161; Voinea et al. J Cell Mol Med 6,465-474).

Antibody treatment of human beings with cancer is known in the art, forexample in U.S. Pat. Nos. 5,736,137; 6,333,410; 5,475,092; 5,585,499;5,846,545; 7,202,346; 6,340,701; 6,372,738; 7,202,346; 5,846,545;5,585,499; 5,475,092; 7,202,346; 7,662,387; 7,662,387; 6,429,295;7,666,425; 5,057,313.

The invention's antibodies may be administered with pharmaceuticallyacceptable carriers, diluents, and/or excipients. Examples of suitablecarriers, diluents and/or excipients include: (1) Dulbecco's phosphatebuffered saline, pH about 7.4, containing about 1 mg/ml to 25 mg/mlhuman serum albumin, (2) 0.9% saline (0.9% w/v NaCl), and (3) 5% (w/v)dextrose.

The invention's antibodies are typically administered in a therapeuticamount. The terms “therapeutic amount,” “pharmaceutically effectiveamount,” “therapeutically effective amount,” and “biologically effectiveamount,” are used interchangeably herein to refer to an amount that issufficient to achieve a desired result, whether quantitative orqualitative. In particular, a pharmaceutically effective amount is thatamount that results in the reduction, delay, and/or elimination ofundesirable effects (such as pathological, clinical, biochemical and thelike) that are associated with disease. For example, a “therapeuticamount that reduces cancer” is an amount that reduces, delays, and/oreliminates one or more symptoms of cancer.

For example, specific “dosages” of a “therapeutic amount” will depend onthe route of administration, the type of subject being treated, and thephysical characteristics of the specific subject under consideration.These factors and their relationship to determining this amount are wellknown to skilled practitioners in the medical, veterinary, and otherrelated arts. This amount and the method of administration can betailored to achieve optimal efficacy but will depend on such factors asweight, diet, concurrent medication and other factors, which thoseskilled in the art will recognize. The dosage amount and frequency areselected to create an effective level of the compound withoutsubstantially harmful effects.

When present in an aqueous dosage form, rather than being lyophilized,the antibody typically will be formulated at a concentration of about0.1 mg/ml to 100 mg/ml.

Depending on the type and severity of the disease, about 0.015 to 15 mgof antibody/kg of patient weight is an initial candidate dosage foradministration to the patient, whether, for example, by one or moreseparate administrations, or by continuous infusion. For repeatedadministrations over several days or longer, depending on the condition,the treatment is repeated until a desired suppression of diseasesymptoms occurs.

The methods of the present invention can be practiced in vitro, in vivo,or ex vivo.

EXPERIMENTAL

The following examples serve to illustrate certain preferred embodimentsand aspects of the present invention and are not to be construed aslimiting the scope thereof.

Example 1

Materials And Methods

The following is a brief description of the exemplary materials andmethods used in the subsequent Examples.

Cell Cultures:

OVCAR3, SKOV3, and A2780 cell lines were obtained through the AmericanType Culture Collection (ATCC, Manassas, Va.) and sustained in cultureaccording to the ATCC literature. For the creation of MUC16+ transfectedcell lines, the carboxyterminus portion of the MUC16 cDNA was introducedas green fluorescent protein fusion proteins using the Vitality phrGFPvector expression system (Stratagene, La Jolla, Calif.). Stable celllines were selected using geneticin (G418, Invitrogen, Grand Island,N.Y.) in their respective culture media and isolated by expression ofGreen Fluorescence Protein. Stable transfectants were routinelymaintained in G418 in their culture media respectively. The ΔMUC16¹¹⁴transfectants have cell surface expression of MUC16 protein from theputative cleavage site to the carboxyterminus (AA 1776 to 1890) (12).

Monoclonal Preparation:

Using the MUC16 sequence, peptide sequences encoding elements of theΔMUC16^(c114) amino acid sequence were synthesized at the MemorialSloan-Kettering Cancer Center (MSKCC) Microchemistry Core Facility. Theinventors synthesized 3 polypeptides (FIG. 1) and modified Polypeptide 1and Polypeptide 2 with a cysteine at the N-terminus for betterconjugation to KLH. Equal concentrations of the KLH-conjugated peptideswere mixed and then used as the immunogen for 5 BALB/c mice. Theinventors selected 1 of the 5 mice whose serum showed the highestreactivity to individual peptides by ELISA, and the MSKCC MonoclonalAntibody Core Facility performed the fusion and selected the antibodiesusing standard protocols. After 10 days of fusion, supernatants wereselected and screened for reactivity by ELISA against the individualsynthetic peptides.

ELISA:

Sandwich ELISA was performed to see the positivity of the antibodies toindividual peptides and GST-ΔMUC16^(c114) fusion protein followingroutine core facility protocol for ELISA assay.

FACS Analyses:

Adherent target cells were removed by 0.05% Trypsin and 0.1% EDTA,washed, and counted by a hemocytometer. Cells were distributed intomultiple Eppendorf tubes with at least 0.5-1×10⁶ cells per tube. Cellswere washed with phosphate buffered saline (PBS) containing 1% FCS and0.025% Sodium Azide (FACS buffer). For internal FACS staining, cells inthe Eppendorf tubes were permeabilized with 1:10 diluted FACSPermeabilizing Solution 2 (BD BioSciences, San Jose, Calif.) for 10minutes at room temperature and then washed twice with ice cold FACSbuffer. Then they were incubated either without (for second antibodycontrol) or with 1 μg/tube of bioreactive supernatants of mouse MUC16monoclonals for 30 minutes on ice. For surface FACS staining, cells wereincubated either without (for second antibody control) or with 1 μg/tubeof bioreactive supernatants of MUC16 monoclonals (9B11.20.16,9C9.21.5.13 and 4H11.2.5), Mouse anti-human OC125 (M3519), Mouseanti-human M11 (M3520) (DakoCytomation, Dako North America Inc.,Carpinteria, Calif.) or VK8 (kindly provided by Dr. Beatrice Yin and Dr.Ken Lloyd, MSKCC, New York, N.Y.) for 30 minutes on ice. Cells inEppendorf tubes were also surface stained with 1 μg/tube of non-specificisotype matched control mouse antibodies (13C4 for IgG1 and 4E11 forIgG2b monoclonals obtained from MSKCC Monoclonal Core Facility) andincubated on ice for 30 minutes. All cells were washed three times withFACS buffer. Cells were incubated with 1 μg/tube of second antibody Goatanti-mouse IgG1-PE or IgG2b-PE for 30 minutes on ice and then washedthree times with FACS buffer. The cells were analyzed by a FACS Caliburmachine at the MSKCC Flow Cytometry Core Facility.

Western Blot Analysis:

Stable cell lines were cultured in 10 cm dishes in their respectiveculture media and incubated with 5% CO₂ at 37° C. for 3 days. They werewashed twice with ice cold PBS to remove the serum-containing media.Adherent cells were scraped with 1-2 ml of ice cold PBS, and the cellswere spun down in an Eppendorf tube at 4° C. in an Eppendorf centrifuge.Supernatant was discarded, and the cells were lysed with 0.2 ml ofmodified Ripa lysis buffer (20 mM Tris-HCL; pH 7.4; 150 mM NaCl; 1%NP-40; 1 mM Na3VO4; 1 mM PMSF; 1 mM DTT; 10 μg/ml leupeptin; and 10μg/ml aprotinin) for 30 minutes on ice and spun at 4° C. for 10 minutes.The soluble solution was separated into a tube and the debris pellet wasdiscarded. Protein concentration was measured using the Bio-Rad ProteinAssay (BioRaD Laboratories, Hercules, Calif.). Equal amounts of proteins(GST-MUC16-CD-fusion protein or stable cell line extracts) wereseparated by sodium dodecyl sulfate polyacrylamide gel electrophoresis(SDS-PAGE) and transferred to nitrocellulose membrane using a BioRadtransfer apparatus in a cold room at 4° C. The membranes were blockedwith 3% bovine serum albumin (BSA) in PBS with 0.1% Tween-20 (PBST) at4° C. overnight. Membranes were probed with primary antibody (1:1000dilution) for 1 hr at room temperature and then washed three times withPBST. Then the membranes were stained with corresponding secondantibody, anti-Mouse IgG Horse Radish Peroxidase (HRP) linked wholeantibody from sheep (GE Healthcare, UK) (1:5000 dilution), for 1 hr atroom temperature. Membranes were washed three times with PBST anddeveloped with a Western Lightning® chemiluminescence reagent (ECL,Perkin Elmer, Waltham, Mass.) for 1-5 minutes at room temperature, andthe signals were developed on Kodak BioMax Film.

Binding and internalization studies with monoclonal antibodies andOVCAR3 and SKOV3 stable transfectants:

Purified monoclonal antibodies were labeled with ¹³¹I using the iodogenmethod and purified by size exclusion chromatography (22). Saturationbinding studies were performed with radiolabeled antibodies usingsubstrates of intact OVCAR-3 cells. Briefly, 10 test solutions wereprepared (in triplicate) and they contained increasing amounts of theradioiodinated antibodies, 3-500 000 cells in a total volume of 500 μLof PBS (0.2% BSA; pH 7.4). The cells were isolated by rapid filtrationthrough a glass fiber membrane and washed with ice cold tris bufferedsaline. Cells were counted in a gamma counter with standards of totalactivity added. For each concentration of radiolabeled antibody,non-specific binding was determined in the presence of 100 nM of theunmodified antibody. The data were analyzed with a least squaresregression method (Origin, Microcal, Software Inc., Northampton, Mass.)to determine the K_(d) and B_(max) values, and a Scatchardtransformation was performed.

Antibody cell internalization studies were performed with ¹³¹I-4H11 and¹³¹I-OC125 monoclonal antibodies and SKOV3-phrGFP-ΔMUC16^(c334) stabletransfected cells. Briefly, radiolabeled antibody (370 MBq/mg, 100 kcpm)in 2 mL of medium was added to SKOV3 cells plated in a 6-well plate. Theplates were incubated at 37° C. for up to 24 hours. At various timepoints, the medium was removed from three wells and the cells washedwith 2×2 mL PBS. Cell surface bound activity was then stripped andcollected with 2×2 mL of an ice cold acid wash (100 mM acetic acid 100mM glycine; pH 3.0). The cells were then dissolved with 2×1 ml 1 M NaOHand collected. At the end of the study all samples were counted with agamma counter together with standards, representing the initial amountof radioactivity added. All the media samples were analyzed by ITLC-SGwith mobile phases of 5% TCA to determine unbound ¹³¹I.

Tissue Microarray (TMA):

Tissue microarrays were either constructed within our institution orbought from a commercial laboratory if not available internally.Briefly, core-needle biopsies of pre-existing paraffin-embedded tissuewere obtained from the so-called donor blocks and then relocated into arecipient paraffin-arrayed “master” block by using the techniques byKononen et al. and subsequently modified by Hedvat et al (23-24). Amanually operated Tissue Arrayer MTA-1 from Beecher Instruments Inc.(Sun Prairie, Wis.) was used to produce sample circular spots (cores)that measured 0.6 to 1.0 mm in diameter. The cores were arrayed 0.3 to0.4 mm apart from each other. A layer of control tissues wasstrategically laid around the actual tissue microarrays in order toavoid edging effects. The specific composition of each tissue microarrayis delineated below. Slides of tissue microarrays for ovarian cancer,prostate cancer, adenocarcinoma of the lung, mucinous neoplasms of thepancreas, and invasive ductal and invasive lobular breast carcinoma wereprepared by cutting 4 um sections from formalin-fixed paraffin-embeddedtissue. Normal adult and fetal tissue microarrays were obtained from acommercial source (Biomax, US). OVCAR3 cells were used as positivecontrols.

Immunohistochemistry:

Immunohistochemistry was performed on the tissue microarrays with bothstandard OC125 (Ventana, Tucson, Ariz.) and the novel monoclonalantibodies. Sections of the tissue microarrays were cut at 4 microns,placed on Superfrost/Plus microscope slides (Fisher brand) and baked ina 60° oven for at least 60 minutes. The slides were then deparaffinizedand hydrated to distilled water, soaked in citrate buffer at pH 6.00 for30 minutes at 97° C., washed in running water for 2-5 minutes, incubatedfor 5 minutes in 3% hydrogen peroxide diluted in distilled water. Slideswere washed in distilled water for 1 minute, transferred to a bath ofphosphate buffered saline (PBS), pH 7.2, for two changes of 5 minuteseach and placed in 0.05% BSA diluted in PBS for a minimum of 1 minute.After drying around tissue sections, normal serum was applied at a 1:20dilution in 2% BSA/PBS and incubated for a minimum of 10 minutes at roomtemperature in a humidity chamber. The serum was then suctioned offwithout allowing the sections to dry, and approximately 150 lambda ofnovel antibody at a dilution of 1:1000 was placed on the tissue. Theslide was incubated overnight (approximately 15-18 hours) at 4° C. in ahumidity chamber. Primary antibody was washed off using three changes ofPBS for 10 minutes each. Secondary antibody, biotinylated α-mouse fromVector laboratories (Burlingame, Ca), was applied at 1:500 dilution in1% BSA/PBS and incubated for 45-60 minutes at room temperature inhumidity chamber. The antibody was washed off again using three changesof PBS as above. Slides were then transferred to a bath ofdiaminobenzidine (DAB), diluted in PBS for 5-15 minutes. The slides werethen washed in tap water for 1 minute, counterstained using Harrismodified hematoxylin (Fisher), decolorized with 1% acid alcohol and bluein ammonia water, dehydrated with 3 changes each of 95% ethanol, 100%ethanol and xylene for 2 minutes each and coverslipped with permanentmounting medium.

Immunohistochemistry Scoring:

Commercially available antibodies, such as OC125 and M11, target complexglycosylation-dependent epitopes. Our hypothesis is that glycosylationmay be tissue specific; therefore, it was important to examine theutility of the peptide-directed antibodies in paraffin-fixed tissues andsurvey the prevalence of MUC16 expression. The three candidateantibodies, 4H11, 9C9 and 4A5, were characterized using OVCAR3 cell linepellets. Of the three, the 4H11 antibody showed the strongest, mostdiffuse and consistent staining pattern at multiple dilutions, with theleast amount of background staining and, therefore, was optimized foruse in human tissues in the pathology core facility.

Using 4H11, the inventors stained and scored positivity using tissuemicroarrays from high-stage, high-grade ovarian serous carcinomas (FIG.2), these tumors being the most common type of ovarian cancer,representing approximately 80-85% of all ovarian carcinomas in Westernindustrialized nations (25). To test the specificity of the novelantibody, the inventors also stained tissue microarrays of cancers ofthe prostate, lung, breast, and pancreas and compared their stainingintensities with that of OC125 monoclonal antibody (FIG. 6A-D). Todetermine whether there would be any cross-reactivity with normal humantissues, the antibodies were also tested on normal human adult and fetalTMAs.

All of the stained sections were reviewed by a reference pathologist(KJP). A subset of cores for which there was equivocal staining was alsoindependently scored by a second pathologist (RAS) to ensure consistencyin scoring methods. Only cytoplasmic and/or membranous staining wasconsidered positive. If a portion of the cell showed membranousstaining, that was considered partial staining. A scoring system wasdevised to provide a semiquantitative assessment of stainingdistribution and intensity in individual cores. At the same time, it wasdesigned to be useful for comparing the staining distribution andintensity between OC125 and the novel antibodies. The score incorporatedthe percentage of cells, the intensity and pattern of the stainingaccording to the following standards: score 0: no staining; score 1: <5%strong or weak; score 2: 5-50% strong or weak; score 3: 51-75% strong or51-100% weak; score 4: 76-99% strong; and score 5: 100% strong staining(FIG. 3A-FIG. 3L). The pathologist first reviewed all tissue microarraysstained with OC125 and scored each core. Then the same cores stainedwith the novel antibodies were scored 1 to several days after OC125without reference to the previous results. Direct comparison of thescoring between the stains for each core was made only after all of thescoring was completed. The same process was used for all non-ovariantissue microarrays. After comparison, core staining was determined to beconcordant, equivocal, or discordant based on the point differentials.Concordant cores differed by 0 to 1 point, equivocal cores differed by 2points, and discordant cores differed by 3 to 5 points. The oneexception to this rule was when the difference of 1 point was between ascore of 0 and 1, in which case, the differences were consideredequivocal. This was in order to truly separate negative cases from evenfocally positive ones.

Example 2

Generation and Characterization of Anti-MUC16 Monoclonal Antibodies

MUC16-directed monoclonal antibodies were isolated by ELISA-basedscreening using both the individual peptides and recombinantGST-ΔMUC16¹¹⁴ protein followed by sequential subcloning for single cellclones.

Tables 1A and 1B: MUC16-carboxyterminus monoclonal antibodies showingtheir reactivity to GST-ΔMUC16^(c114) western, FACS analysis on OVCAR3wild type cells

TABLE 1A Peptide 1 Peptide 2 Peptide 3 (1:10) (1:10) (1:10) ELISA GST-ELISA GST- ELISA GST Hybridoma MucCD (1:1) Hybridoma MucCD (1:1)Hybridoma MucCD (1:1) Sups Western OVCAR3 Sups Western OVCAR3 SupsWestern OVCAR3 (1:1) +/− FACS +/− Isotype (1:1) +/− FACS +/− Isotype(1:1) +/− FACS +/− Isotype 10A2 + − IgG1, IgM 13H1 Weak − IgG1 22E10 + −IgG2b 23D4 − − missing 28F8 + + IgG1, IgM 22F11 Weak − IgM 2F4 Weak −IgG1, IgM 11B6 − − IgM 19G4 Weak − IgG1, IgM 9B11 Weak +/− IgG1 4C7 + −IgG1 31A3 Weak − IgG1 23D3 Weak + IgG1, IgG2 28F7 + + IgG1 4C2 + − IgG1,IgM 30B1 − − IgG1 9C7 + + IgG1 27G4 + − IgM 31B2 + − IgM 9C9 + + IgG1,IgG2b 19D1 + − IgG2b 4H11 + + IgG2b, IgM 22F1 + − IgG2b, IgM 4A2 − −IgG1 4D7 + − IgG3 4A5 + + IgG1 9A5 − − IgM 29G9 + − IgG1 31C8 − − IgG2b5C2 + + IgG1 6H2 Weak − IgG1, IgM 23G12 − − IgG1, IgG2a 10F6 − − IgG125G4 − − IgG1, IgM 3H8 + − IgG1, IgM 26B2 + + IgG1, 24G12 − − IgG1, IgMIgG2b, IgM 25H3 − − IgG1, IgM

TABLE 1B Peptide 1 Peptide 2 Peptide 3 OVCAR3 OVCAR3 OVCAR3 FACS +/−Isotype FACS +/− Isotype FACS +/− Isotype 9B11.20.16 +/− IgG19C9.21.5.13 + IgG2b 31A3.5.1 − IgG1 4H11.2.5 + IgG2b 9C7.6 + IgG15C2.17 + IgG1 4A5.37 + IgG1 28F7.18.10 + IgG1

TABLE 2 Antibodies specific for exemplary portions of MUC161. Muc16 Polypeptide 1: 14394 14410 (MUC16 sequence)NFSPLARRVDRVAIYEE (SEQ ID NO: 01) 17 aaMouse monoclonals which are specific to this peptide are:9B11.20.16 (IgG1) 10A2 (IgG1, IgM) 2F4 (IgG1, IgM) 23D3 (IgG1, IgG2b)30B1 (IgG1) 31B2 (IgM) 2. Muc16 Polypeptide 2: 14425 14442(MUC16 sequence) TLDRSSVLVDGYSPNRNE (SEQ ID NO: 02) 18 aaMouse monoclonals which are specific to this peptide are:4H11.2.5 (IgG2b) 13H1 (IgG1) 29G9 (IgG1) 9C9.21.5.13 (IgG2b)28F8 (IgG1, IgM) 23G12 (IgG1, IgG2a) 9C7.6 (IgG1) 11B6 (IgM)25G4 (IgG1, IgM) 5C2.17 (IgG1) 4C7 (IgG1) 26B2 (IgG1, IgG2b, IgM)4A5.37 (IgG1) 4A2 (IgG1) 25H3 (IgGl, IgM) 28F7.18.10 (IgG1)3. Muc16 Polypeptide 3 (SEQ ID NO: 03) 14472 14492 (MUC16 sequence)CGVLVTTRRRKKEGEYNVQQQ 21 aaMouse monoclonals which are specific to this peptide are:31A3.5.1 (IgG1) 19D1 (IgG2b) 10F6 (IgG1) 22E10 (IgG2b) 22F1 (IgG2b, IgM)3H8 (IgG1, IgM) 22F11 (IgM) 4D7 (IgG3) 24G12 (IgG1, IgM)19G4 (IgG1, IgM) 9A5 (IgM) 4C2 (IgG1, IgM) 31C8 (IgG2b) 27G4 (IgM)6H2 (IgG1, IgM) 14452 14475FWAVILIGLAGLLGLITCLICGVL (SEQ ID NO:14) is Transmembrane region 24 aa4. Muc16 Polypeptide 4 (SEQ ID NO: 15) containing a cysteine loop polypeptide (SEQ ID NO: 19):14367 14398 (MUC16 sequence)

32 aa Mouse monoclonals which are specific to this peptide are:24B3 (IgM) 9C7 (IgM)

IgM kappa

IgM kappa

IgM kappa

IgM kappa

IgM, IgG1, IgG2b, kappa

IgM, IgG1, kappa

IgM, kappa

IgG1 kappa

IgG1 kappa

IgG1 kappa

IgM, IgG1, IgG3, IgG2a, kappa

IgM, kappa, lambda

IgM kappa

IgG1, IgG2b

IgM kappa

IgM kappa 19D3 IgM kappa

IgM, IgG1, IgG2b, kappa

IgM kappa

IgG3, IgM kappa

IgM, IgG3, IgG2b, IgG2a, IgG1, kappa

IgG2a, IgG3, kappa

IgM, kappa

light kappa only

IgM, kappa

IgM, kappa

IgM, kappa

IgM, kappa

IgM, kappa

IgM, kappa

IgM, kappa

IgM, kappa

IgG2a, IgM, kappa

IgM, kappa

IgM, kappa

The identified monoclonal antibodies are listed in Table 1A and Table 2.Each of the selected monoclonal antibodies was reactive againstGST-ΔMUC16^(c114). The commercial MUC16-directed antibodies (OC125, M11,or VK8) did not bind to GST-ΔMUC16^(c114) in ELISA or Western blotting.The clones were tested in FACS against OVCAR3 ovarian cancer cells andin Western blot analysis against GST-ΔMUC16^(c114) (Table 1B), andselected purified monoclonal antibodies were isolated.

The inventors used the OVCAR3 wild type and the SKOV3 cells transducedwith phrGFP-ΔMUC16^(c114) to characterize the selected antibodies byFACS analysis. All of the selected monoclonal antibodies bound to bothcell lines while commercial VK8, M11 and OC125 antibodies bound to theOVCAR3 cells but not to the SKOV3-phrGFP-ΔMUC16^(c114) cell line. Theantibodies against Polypeptide 3 required permeabilization since it isan internal epitope (FIGS. 7A-7F).

Western blot analysis using the GST-ΔMUC16^(c114) purified proteinshowed strong binding with 4H11 and 9C9 antibodies (FIG. 4A), while theother selected antibodies showed less binding. TheSKOV3-phrGFP-ΔMUC16^(c114) transfectant was also positive by Westernblot analysis using 4H11 and 9C9 antibodies (FIG. 4B). As before, thecommercial antibodies did not interact with the GST-ΔMUC16^(c114)purified protein or cell lysates of the SKOV3-phrGFP-ΔMUC16¹¹⁴ cellline.

The binding of six monoclonal antibodies against OVCAR3 MUC16 wereexamined in affinity binding studies. Three antibodies—9C7, 5C2 and28F7—showed only modest levels of binding compared to the nonspecificbinding of these antibodies to the OVCAR3 cells, which carry largenumbers of MUC16 binding sites. In contrast, 4H11, 9C9, and 4A5monoclonal antibodies showed highly specific binding affinity, as shownin FIGS. 5A-5D, with binding affinities of 6.8-8.6 nM against the cellsurface epitopes of OVCAR3 cells. The inventors also examined theinternalization of antibody bound to cell surface MUC16 protein. Theinventors examined internalization in the transfectedSKOV3-phrGFP-ΔMUC16^(c334) cell line which bears the carboxy terminus ofMUC16, including the 4H11 epitope and a single degenerate tandem repeatsequence to interact with the OC125 antibody. The commercial antibodiesOC125, M11, and VK8 all bind to the cell surface of this transduced cellline. The ¹³¹I-labeled 4H11 showed rapid internalization at a highlevel, whereas ¹³¹I-labeled OC125 antibody was internalized at a muchlower rate (FIG. 5E).

Example 3

Immunohistochemistry Results:

Given their highly specific binding affinities, the antibodies 9C9, 4A5,and 4H11 were characterized for utility in immunohistochemistry usingOVCAR3 cell lines. Of the three, the 4H11 antibody was selected to beoptimized for use in human tissues based on its robust, sensitive andspecific staining pattern as compared to the other two antibodies.

A. Ovary

Two high-stage, high-grade ovarian serous carcinoma tissue microarrayslides composed of 419 cores, representing primary, metastatic andrecurrent tumors from 40 patients were stained with both OC125 and 4H11monoclonal antibodies (FIG. 2). The OC125 tissue microarrays showed 279(66%) cores with 3-5 staining, 99 (24%) with 1-2 staining, and 41 (10%)with no staining. The 4H11 tissue microarrays showed 236 (56%) with 3-5staining, 91 (22%) with 1-2 staining, and 92 (22%) with no staining. Thetwo antibodies were concordant in 233 (56%) cores, equivocal in 161(38%), and discordant in 25 (6%). Of the 25 discordant cores, 12 (48% ofdiscordant cases, 3% of all cases) showed greater 4H11 positivity thanOC125. Nine were discordant by a difference of 4 points, and 3 werediscordant by a difference of 5 points. There was a total of 186discordant and equivocal cores together, 48 (26%) of which showedgreater staining with 4H11 than OC125. The staining pattern of both 4H11and OC125 was cytoplasmic and membranous, although the membranouspattern of OC125 was stronger and better defined than 4H11 in themajority of cases. Discordant cases demonstrated higher levels of 4H11than other cases.

B. Breast Cancer

A variety of other tissues were also examined for 4H11 staining to testthe antibody's specificity. Of the 50 cores of invasive ductalcarcinomas of the breast (number of patients unavailable), only 2 (4%)showed a score of 4 or greater 4H11 staining and none had scores of 3-5for OC125 staining. The staining pattern with OC125 was mostlyapical/luminal with some granular cytoplasmic staining. Some tumors withintracytoplasmic lumina also picked up the OC125 stain. 4H11 showed amore diffuse cytoplasmic blush without membranous accentuation.

In contrast, the invasive lobular breast carcinoma tissue microarray(composed of 179 cores with viable tumor, number of patientsunavailable) had frequent MUC16 staining with 4H11. In this tissuemicroarray, 168 cores (94%) showed no staining for OC125, 5 (3%) showed1-2 staining, and only 6 (3%) showed a staining intensity of 3. 4H11staining was different in its distribution pattern, with 49 (27%)showing no staining, 81 (45%) showing 1-2 staining, and 49 (27%) showing3-4 staining. Neither OC125 nor 4H11 had cores with a staining intensityof 5. The staining pattern was of cytoplasmic, luminal/membranous, orintraluminal for both OC125 and 4H11. The intraluminal pattern wasstrong and intense for both stains and highlighted the intracytoplasmiclumen that is commonly present in lobular carcinomas. The concordancerates were 34% concordant, 43% equivocal, and 23% discordant. Of theequivocal and discordant cases, there was none in which the OC125 wasgreater than the 4H11. All 42 discordant cases and 76 of 77 equivocalcases had 4H11 greater than OC125. There was also focal luminal stainingwith 4H11 in benign breast ducts and lobular carcinoma in situ.

C. Lung, Pancreatic and Prostatic Adenocarcinomas

Tumors from other organs were not reactive with either antibody. Thelung adenocarcinoma TMA had 237 cores from 86 patients containing viabletumor. In the pancreatic TMA there were 92 cores from 21 patientscontaining pancreatic mucinous tumors, including intraductal papillarymucinous neoplasms (IPMN) and invasive ductal carcinomas. In theprostate cancer TMA there were 169 cores (number of patients notavailable). None of these cancer tissue microarrays had significantbinding to either OC125 or 4H11. This information is summarized in Table3.

TABLE 3 Staining intensity of OC125 as compared to 4H11 in tissuemicroarrays OC125 vs. 4H11 staining intensity score (%) Site 0 1-2 3-5OC125 4H11 OC125 4H11 OC125 4H11 Ovary high grade 10 28 24 22 66 56serous Breast invasive ductal 68 78 32 18 0 4 Breast invasive lobular 9427 3 45 3 27 Lung adenocarcinoma 63 77 24 18 13 5 Pancreas mucinous 9888 2 10 0 2 neoplasms Prostate 0 0 0 0 0 0 adenocarcinoma Score 0: 0%staining; 1: <5% strong or weak; 2: 5-50% strong or weak; 3: 51-75%strong or 51-100% weak; 4: 76-99% strong; 5: 100% strong

D. Normal Tissues

There was no staining with OC125 or 4H11 in normal adult colon, rectum,ectocervix, small intestine, ovary, liver, pancreatic ducts, spleen,kidney, and skin. OC125 and 4H11 both stained endocervical glands (OC125luminal, 4H11 weak cytoplasmic), esophageal glands (luminal), bronchialepithelium (OC125 luminal, 4H11 intracytoplasmic granules), and thymiccorpuscles (cytoplasmic). 4H11 demonstrated weak to moderate staining ofthe gastric glands, particularly at the crypts, with an intracytoplasmicgranular pattern. Other organs that showed punctuate intracytoplasmicstaining with 4H11 only were prostate, seminiferous tubules of thetestes, and the islet cells of the pancreas. The staining in thepancreatic islets cells was particularly strong and consistent. Therewas also nonspecific staining of liver, kidney and brain with 4H11.There were no cases that stained with OC125 and not 4H11.

Similarly, there was no staining with either OC125 or 4H11 in fetalheart, gallbladder, colon, small intestine, liver, rectum, adrenal,thyroid, spleen, skin, bone, epididymis, brain, lung, muscle, smoothmuscle, kidney, eye, umbilical cord, and placenta. OC125 only stainedthymic corpuscles in a pattern similar to that in adult tissue. 4H11stained both fetal pancreatic endocrine cells and endocervical glands ina similar pattern to that of their adult counterparts. Islet cellsshowed a granular cytoplasmic pattern, and endocervical glands showed alinear luminal pattern, which was more similar to the OC125 pattern inthe adult tissue.

Example 4

Successful Eradication of Established Peritoneal Ovarian Tumors inSCID-Beige Mice Following Adoptive Transfer of T Cells GeneticallyTargeted to the MUC16 Antigen.

Purpose:

Most patients diagnosed with ovarian cancer will ultimately die fromtheir disease. For this reason, novel approaches to the treatment ofthis malignancy are needed. Adoptive transfer of a patients own T cells,genetically modified ex vivo through the introduction of a gene encodingan chimeric antigen receptor (CAR), an artificial T cell receptor,targeted to a tumor associated antigen, is a novel and promisingapproach to cancer therapy applicable to the treatment of ovariancancer.

Experimental Design:

We have generated several CARs targeted to the retained extracellulardomain of MUC16, termed MUC-CD, an antigen highly expressed on amajority of ovarian carcinomas. We investigate the in vitro biology ofhuman T cells retrovirally transduced to express these CARs byco-culture assays on artificial antigen presenting cells (AAPCs)generated from NIH3T3 fibroblasts genetically modified to express thetarget MUC-CD antigen, as well as by cytotoxicity assays utilizing thehuman OV-CAR3(MUC-CD) ovarian tumor cell line and primary patient tumorcells. Finally, we assess the in vivo anti-tumor efficacy of MUC-CDtargeted T cells in a SCID-Beige orthotopic, xenogeneic OV-CAR3(MUC-CD)murine tumor model.

Exemplary sequences used in this work are in FIG. 17-19.

Results:

CAR modified MUC-CD targeted T cells derived from both healthy donorsand ovarian cancer patients exhibited efficient in vitro cytolyticactivity against both human ovarian cell lines as well as primaryovarian carcinoma cells. MUC-CD targeted T cells may be further expandedex vivo through multiple cycles of co-culture on 3T3(MUC-CD/B7.1) AAPCs.Expanded MUC-CD targeted T cells infused into SCID-Beige mice bearingintraperitoneal human OV-CAR3(MUC-CD) tumors either delayed progressionor fully eradicated tumor even in the setting of advanced disease.

Conclusion:

These promising pre-clinical studies justify further investigation ofMUC-CD targeted T cells as a potential therapeutic approach in theclinical setting treating patients with high risk MUC-16⁺ ovariancarcinomas.

Introduction

Ovarian cancer is the sixth most common cancer worldwide and the seventhleading cause of cancer-related deaths in women (1, 2). Despitemultimodality therapy with surgery and chemotherapy, most patients withovarian carcinomas have a poor prognosis. For this reason, alternativeapproaches to treating this disease are urgently needed.

Infusion of a patient's own T cells genetically targeted ex vivo toantigens expressed on the surface of tumor cells is a promising novelapproach to the adoptive immunotherapy of cancer, and one which has onlyrecently been explored in earnest in the clinical setting. T cells maybe genetically modified to target tumor associated antigens through theretroviral introduction of genes encoding artificial T cell receptorstermed chimeric antigen receptors (CARs). Genetic engineering of T cellsto express artificial T cell receptors that direct cytotoxicity toward atumor cell presents a means to enhance immune recognition andelimination of cancer cells. CARs are most commonly composed of a singlechain fragment length antibody (scFv), derived from a murine monoclonalantibody targeting a given tumor associated antigen, fused to atransmembrane domain (typically CD8, CD28, OX-40, and 4-1BB), fused tothe TCR ζ chain cytoplasmic signaling domain (3-13). When used toreprogram T-cell specificity, these fusion receptors permit recognitionof native antigen. When expressed by the T cells, the resultingconstruct, upon engagement with the targeted antigen, induces T cellactivation, proliferation, and lysis of targeted cells. These fusionreceptors transduce a functional antigen-dependent co-stimulatory signalin primary T cells, permitting sustained T-cell proliferation when bothendogenous TCR and a chimeric receptor for stimulatory signaling areengaged. To date, preclinical studies utilizing CAR-modified T cellshave demonstrated promising results in a wide variety of malignancies(3, 4, 11, 14-18). More recently this approach been investigatedclinically in the form of phase I trials (6, 19-21). These geneticapproaches offer a means to enhance immune recognition and eliminationof cancer cells.

Ovarian carcinomas appear to be relatively immunogenic tumors capable ofinducing an endogenous immune response based on the fact that long-termprognosis of patients is markedly influenced by the degree and qualityof the endogenous immune response to the tumor. Specifically, it hasbeen well documented that the presence of endogenous effector T cellswithin the ovarian cancer tumor microenvironment directly correlates toprolonged patient survival (22-25). In contrast, increasing numbers ofimmune suppressive CD4⁺ CD25^(hi) regulatory T cells (Tregs) within thetumor, which in turn presumably abrogate the anti-tumor activity ofinfiltrating effector T cells, correlates with shorter patient survival(26-29). In fact, it appears that it is the ratio of Tregs to effector Tcells within the tumor microenvironment which ultimately dictateswhether the endogenous immune response to the cancer is of benefit ordetriment to the patient (24, 28). In this setting, the ability togenerate and subsequently expand a population of tumor targeted effectorT cells ex vivo which are subsequently infused back into the patient,may in turn skew the Treg to effector T cell ratio to one more favorableto eradicating the disease.

Mucins are important biomolecules for cellular homeostasis andprotection of epithelial surfaces. Changes to expression of mucins inovarian cancer might be exploited in diagnosis, prognosis and treatment(1). MUC16 is one such mucin which is over expressed on most ovariancarcinomas and is an established surrogate serum marker (CA-125) for thedetection and progression of ovarian cancers (30-33). MUC16 is ahigh-glycosylated mucin composed of a large cleaved and released domain,termed CA-125, consisting of multiple repeat sequences, and a retaineddomain (MUC-CD) which includes a residual non-repeating extracellularfragment, a transmembrane domain, and a cytoplasmic tail (34). Since theantigen is otherwise only expressed at low levels in the uterus,endometrium, fallopian tubes, ovaries, and serosa of the abdominal andthoracic cavities, MUC16 is a potentially attractive target forimmune-based therapies.

However, the fact that most of the extracellular domain of MUC16 iscleaved and secreted limits the utility of MUC16 as a target antigen onovarian carcinomas. In fact, to date, all reported MAbs to MUC16 bind toepitopes present on the large secreted CA-125 fraction of theglycoprotein, with none known to bind to the retained extra-cellularfraction (MUC-CD) of the antigen (35-37). Since the MUC-CD fraction ofthe antigen is retained on cell surface, generating T cells specific tothis portion of MUC16 may largely overcome the limitation of MUC16 as atarget for adoptive cellular immunotherapy. To this end, we havepreviously generated a series of murine MAbs specific to the retainedMUC-CD extracellular domain (38). Utilizing a hybridoma which expressesone such MAb, 4H11, we have successfully constructed several CARsspecific to the MUC-CD antigen. This invention provides a nucleic acidencoding a chimeric T cell receptor, composed of, at least a zeta chain,a signaling region and a binding element that specifically interactswith a selected target as well as the chimeric T cell receptorcomprising a zeta chain portion, a signaling region and a bindingelement.

In this report, we demonstrate highly efficient retroviral transductionof these MUC-CD targeted CARs into human T cells with resulting T cellsable to specifically target and lyse MUC-CD⁺ tumor cells in vitro.Furthermore, we demonstrate efficient MUC-CD targeted T cell expansionin vitro through repeated co-culture on NIH (3T3) fibroblastsgenetically modified to express MUC-CD and the co-stimulatory ligandB7.1 (CD80). Successful expansion of modified T cells allowed us tosubsequently generate sufficient T cell numbers to conduct in vivostudies in immune compromised SCID-Beige mice bearing establishedintraperitoneal MUC-CD⁺ human ovarian tumors. Significantly, in thesestudies we demonstrate marked anti-tumor efficacy of MUC-CD targeted Tcells, both following direct intraperitoneal as well as intravenousinjection when compared to either untreated mice, or mice treated with Tcells bearing a CAR targeted to an irrelevant antigen. In addition, wedemonstrate significant cytotoxicity of 4H11-28z⁺ patient's T cells andhealthy donor's T cells targeting primary ascites-derived ovariancarcinoma cells from cancer patients.

To our knowledge this is the first report wherein T cells geneticallytargeted to the MUC16 antigen demonstrate marked anti-tumor efficacyagainst MUC16⁺ tumors either in vitro or in vivo. These data serve as arationale for proposing future clinical trials utilizing this approachin patients with high risk ovarian carcinomas.

Materials and Methods

Cell Lines and T Cells

The OV-CAR3 tumor cell line was cultured in RPMI 1640 (Invitrogen, GrandIsland, N.Y.) supplemented with 10% heat-inactivated FBS, nonessentialamino acids, HEPES buffer, pyruvate, and BME (Invitrogen). The PG13 andgpg29 retroviral producer cell lines were cultured in DMEM (Invitrogen)supplemented with 10% FCS, and NIH-3T3 artificial antigen-presentingcells (AAPC), described previously (3), were cultured in DMEMsupplemented with 10% heat-inactivated donor calf serum. T cells wereobtained from peripheral blood of healthy donors under IRB approvedprotocol #95-054, in BD Vacutainer CPT tubes (Becton Dickinson, FranklinLakes, N.J.) as per the manufacturers instructions. All media weresupplemented with 2 mmol/L L-glutamine (Invitrogen), 100 units/mLpenicillin, and 100 μg/mL streptomycin (Invitrogen). T cells werecultured RPMI 1640 media as above supplemented with 20 IU/ml IL-2(Novartis Pharmaceuticals, East Hanover, N.J.) and where indicated,medium was supplemented with 10 ng/mL interleukin 15 (R&D Systems,Minneapolis, Minn.).

Isolation of Patients Ascites-Derived Cancer Cells

Primary human ascites-derived cancer cells were obtained from ovariancancer patients undergoing surgery for newly diagnosed advanced serousovarian carcinoma under IRB approved protocol #97-134. The tumor cellswere isolated from ascitic fluid of patients by centrifugation at 600 gfor 10 min at room temperature. Cells were washed once with 1×PBS andcultured in RPMI 1640 media supplemented with 10% FBS for futureanalysis.

Generation of the MUC-CD Targeted 4H11z and 4H11-28z CARs

The heavy and light chain variable regions of the 4H11 monoclonalantibody were derived from the hybridoma cell line 4H11. Utilizing cDNAgenerated from 4H11 RNA we isolated the V_(H) coding region by RACE PCRutilizing modified primers as described elsewhere (39, 40). The V_(L)chain variable region was cloned by standard PCR utilizing modifiedprimers as described by Orlandi et al (41, 42). The resulting V_(H) andV_(L) fragments were subcloned into the TopoTA PCR 2.1 cloning vector(Invitrogen) and sequenced. The V_(H) and V_(L) fragments weresubsequently ligated to a (Gly₄Ser)₃ spacer domain, generating the 4H11scFv and fused to the human CD8 leader peptide (CD8L) by overlapping PCR(9, 41). In order to construct the MUC-CD targeted 4H11 CARs, the codingregion of the CD8L-4H11 scFv was fused to the human CD8 hinge andtransmembrane domains (to generate the 4H11z CAR), or alternatively tothe CD28 transmembrane and cytoplasmic signaling domains (to generatethe 4H11-28z CAR), fused to the T cell receptor CD3ζ-signaling domain(3, 9, 43). The resulting CAR constructs were subsequently sub-clonedinto the modified MMLV retroviral vector SFG (44). VSV-G preudotypedretroviral supernatants derived from transduced gpg29 fibroblasts wereused to construct stable PG13 gibbon ape leukemia virus (GaLV)envelope-pseudotyped retroviral producing cell lines (41).

Retroviral Gene Transfer

Isolated healthy donor peripheral blood mononuclear cells (PBMCs) wereactivated with phytohemagglutinin (PHA) at 2 μg/ml (Sigma. St. Louis,Mo.) and retrovirally transduced on retronectin coated non-tissueculture plates (45). Briefly, six-well non-tissue culture plates (BDBiosciences, San Jose, Calif.) were coated with RetroNectin (RN) (TakaraBiomedicals, Otsu, Japan) as per manufacturer's instructions.Forty-eight hours after PHA activation, aliquots of 1×10⁶ T cells in 1ml of supplemented RPMI medium were placed in each well of the RN-coatedplates, along with 1 ml of SFG retroviral supernatant. T cells werecentrifuged daily for 3 consecutive days with fresh retroviralsupernatant added daily at 2000 g at 30° C. for 1 hr (45). Gene transferwas assessed on day 7 by FACS.

In order to generate the relevant NIH-3T3 murine fibroblast artificialantigen presenting cells, a MUC-CD construct encoding the retainedextracellular, transmembrane and cytoplasmic domains of the MUC-16antigen was initially subcloned into SFG retroviral vector, SFG(MUC-CD).3T3(MUC-CD) AAPCs were generated by retroviral transduction ofSFG(MUC-CD) into wild-type NIH-3T3 fibroblasts, while 3T3(MUC-CD/B7.1)AAPCs were generated by retroviral transduction of previouslyestablished 3T3(B7.1) fibroblasts (41, 46). Highly enriched cell lineswere isolated by FACS.

To generate the OV-CAR3(MUC-CD) and OV-CAR3(MUC-CD/GFP-FFLuc) celllines, we retrovirally transduced the WT OV-CAR3 human ovarian cancercell line with SFG(GFP-FFLuc) as described previously (47) and/orSFG(MUC-CD) VSV-G pseudotyped retroviral supernatants derived from gpg29fibroblasts as described elsewhere (44). Resulting tumor cells weresorted by FACS for either MUC-CD expression alone for the OVCAR3(MUC-CD)cell line, or dual MUC-CD and GFP expression for theOVCAR3(MUC-CD/GFP-FFLuc) cell line. MUC-CD expression by FACS wasassessed using the 4H11 MAb.

In Vitro Analyses of CAR⁺ Human T Cells

To assess in vitro expansion and cytokine release upon stimulation,transduced T cells were co-cultured for 7 days after retroviraltransduction in 6-well tissue culture plates (BD Biosciences) onconfluent NIH 3T3 AAPCs in RPMI medium supplemented with 10% FBS in theabsence of supplemented cytokines. In order to generate sufficientnumbers of CAR-modified T cells for in vivo studies, transduced T cellswere co-cultured on B7.1⁺ AAPCs (3T3(MUC-CD/B7.1)) in RPMI mediumsupplemented with 20 IU IL-2/mL and 10 ng/mL IL-15 as describedpreviously (3, 43). Patients T cells were activated and expanded withhuman CD3/CD28 beads (DYNAL®, Invitrogen, Carlsbad, Calif.) followingmanufacturer's recommendations.

Western Blot Analysis of CAR Expression

Western blot analysis of T-cell lysates under reducing conditions with0.1 mol/L DTT (Sigma) was performed as previously described (46).Briefly, transduced T cells were washed in PBS and resuspended inradioimmunoprecipitation assay (RIPA) buffer (Boston BioProducts,Worcester, Mass.) with mini complete protease inhibitor as per themanufacturer's instructions (Roche Diagnostics, Indianapolis, Ind.).Resulting proteins were separated on 12% SDS-PAGE mini gels (Bio-Rad,Hercules, Calif.) after the addition of 6× reducing loading buffer(Boston BioProducts, Worcester, Mass.) and heating at 100° C. for 10min. Separated proteins were subsequently transferred to Immobilonmembranes and probed using an anti-human CD3C chain monoclonal antibody(BD Biosciences). Antibody binding was detected by probing the blot withgoat anti-mouse horse radish peroxidase-conjugated antibody followed byluminescent detection using Western Lighting Chemiluminescence ReagentPlus (Perkin-Elmer Life Sciences, Boston, Mass.) as per themanufacturer's instructions.

Cytotoxicity Assays

In vitro modified T cell cytotoxicity was assessed using the DELFIA®EuTDA assay (PerkinElmer LAS, Inc, Boston, Mass.) followingmanufacturer's recommendations. Cytotoxocity was assessed at 2 hours ateffector T cell to target OV-CAR3(MUC-CD) or primary tumor cells (E:T)at indicated ratios. Effector T cells in these assays represent thenumber of CD8⁺ CAR⁺ T cells.

Cytokine Detection Assays

Cytokine assays were performed as per manufacturer's specificationsusing a multiplex Human Cytokine Detection assay to detect IL-2 and IFNγ(Millipore Corporation, Billerica, Mass.) utilizing the Luminex IS 100system. Cytokine concentrations were assessed using IS 2.3 software(Luminex Corp., Austin, Tex.).

In Vivo SCID-Beige Mouse Tumor Models

In all in vivo studies, 8-12 week-old FOX CHASE C.B.-17 (SCID-Beigemice) (Taconic, Hudson, N.Y.) were initially injected ip with either3×10⁶ OV-CAR3(MUC-CD), or for bioluminescent imaging (BLI) studies 3×10⁶OV-CAR3(MUC-CD/GFP-FFLuc) tumor cells. Subsequently, 3×10⁷ CAR⁺ T cellswere injected ip or iv on day 1 or 7 following tumor injection asindicated. Mice were monitored for distress as assessed by increasingabdominal girth, ruffled fur, and decreased response to stimuli.Distressed mice were euthanized. All murine studies were done in contextof an Institutional Animal Care and Use Committee-approved protocol(#00-05-065).

Bioluminescent Imaging (BLI) of OVCAR3(MUC-CD/GFP-FFLuc) Tumor Cells inSCID-Beige Mice

BLI was performed using Xenogen IVIS imaging system with Living Imagesoftware (Xenogen; Alameda, Calif.). Briefly, OVCAR3(MUC-CD/GFP-FFLuc)tumor bearing mice were injected by ip with D-luciferin (150 mg/kg;Xenogen) suspended in 200 μl PBS and imaged under 2% isofluraneanesthesia after 10 min. Image acquisition was done on a 25-cm field ofview at medium binning level for 0.5-min exposure time (3, 43).

Flow Cytometry

All flow cytometric analyses of T cells and tumor cells was performedusing a FACScan cytometer with Cellquest software (BD Biosciences). Tcells were analyzed using CAR-specific polyclonal goat Alexa Fluor 647antibody (Molecular probes, Eugene, Oreg.) phycoerythrin-labeledanti-human CD4, CD8, B7.1 (Caltag Laboratories, Burlingame, Calif.),B7.2 (Invitrogen, Camarillo, Calif.), 4-1BBL, and OX40 antibodies(Ancell Corporation, Bayport, Minn.). 3T3(MUC-CD) and OV-CAR3(MUC-CD)cells were stained with Alexa Fluor 647 labeled 4H11 antibody (generatedand labeled in the MSKCC monoclonal antibody core facility).

CFSE Labeling of CAR⁺ T Cells

CAR⁺ T cells were stained with CFSE using the CellTrace™ CFSE cellproliferation kit following manufacturer's recommendations (MolecularProbes, Eugene, Oreg.). Proliferation of CFSE labeled T cells wasanalyzed by FACS. For detection of CFSE labeling T cells in vivo,ovarian tumors were macerated through 40 μm cell strainer (BD Falcon,Franklin Lakes, N.J.) and washed twice with 2% FBS/PBS before antibodystaining and FACS analysis.

Statistics

Survival data assessed by log-rank analysis using GraphPad Prismsoftware (GraphPad Prism software, San Diego, Calif.). Cytokine datawere analyzed by Student's one-tailed t-test.

Results

We have constructed SFG retroviral vectors encoding first (4H11z) andsecond generation (4H11-28z) CARs targeted to the MUC-CD antigen usingthe 4H11 hybridoma which generates a MAb specific to the MUC-CD antigen(FIG. 11A). We confirmed expression of appropriately sized CAR proteinsby Western blot analysis of resulting PG-13 retroviral producer cells(SFG-4H11z and SFG-4H11-28z) probed with a ζ-chain specific antibody(data not shown).

In order to assess the function of the first generation 4H11z CAR,healthy donor T cells isolated from peripheral blood were retrovirallytransduced to express the 4H11z and control 19z11 CARs (FIG. 11B).Function of the 4H11z CAR was assessed by proliferation of 4H11ztransduced T cells following co-culture on 3T3(MUC-CD/B7.1) AAPCs.Results demonstrate specific proliferation of 4H11z transduced T cells,when compared to 19z11 modified T cells (FIG. 11C). These data areconsistent 4H11z CAR mediated specific binding to the MUC-CD antigen andsubsequent T cell activation.

Since most malignancies fail to express co-stimulatory ligands, wefurther modified the 4H11z CAR to express the CD28 transmembrane andcytoplasmic co-stimulatory signaling domains, constructing the secondgeneration 4H11-28z CAR (FIG. 11A). To assess whether the 4H11-28z CAR,when expressed by human T cells, was capable of generating both aprimary activating signal (termed “signal 1”) through the ζ chain, aswell as a co-stimulatory signal (termed “signal 2”) through the CD28cytoplasmic domain, which in turn allows for efficient T cellproliferation in the absence of exogenous co-stimulatory ligands, wecompared T cell proliferation following co-culture on either 3T3(MUC-CD)or 3T3(MUC-CD/B7.1) AAPCs in the absence of exogenous cytokines. Asexpected, the second generation 4H11-28z⁺ T cells markedly expanded whencompared to 4H11z⁺ T cells upon co-culture with 3T3(MUC-CD) AAPCs. Incontrast, both 4H11z⁺ and 4H11-28z⁺ T cells expanded similarly on3T3(MUC-CD/B7.1) AAPCs (FIG. 12A). Co-stimulation mediated by the4H11-28z CAR was further verified by analysis of day 2 tissue culturesupernatants from co-culture experiments on 3T3(MUC-CD) AAPCsdemonstrating enhanced IL-2 secretion, a cytokine typically secreted inthe context of T cell co-stimulation, when compared to control 19z1+ and19-28z⁺ T cells and first generation 4H11z⁺ T cells (FIG. 12B).Secretion of IFNγ was comparable between 4H11z⁺ and 4H11-28z⁺ activatedT cells.

We next assessed the ability of MUC-CD targeted T cells to expandfollowing weekly re-stimulations through co-culture on 3T3(MUC-CD/B7.1)AAPCs in the context of exogenous IL-2 and IL-15 (3). Both 4H11z⁺ and4H11-28z⁺ T cells expanded greater than 2 logs over 3 weeks (FIG. 12C).T cells transduced with the 4H11-28z were further analyzed by FACS forCAR expression 7 days after initial activation on AAPCs and followingtwo subsequent co-stimulations on AAPCs demonstrating an expectedenrichment of the CAR⁺ T cell fraction (FIG. 12D). Similar data wasgenerated with expanded 4H11z⁺ T cells (data not shown).

In Vitro Cytotoxicity and Proliferation of MUC-CD Targeted T CellsFollowing Co-Culture with OV-CAR3(MUC-CD) and Freshly Isolated AscitesDerived Ovarian Tumor Cells.

In order to assess the ability of 4H11z⁺ and 4H11-28z⁺ T cells to targetand lyse human ovarian carcinoma tumors, we utilized the human OV-CAR3cell line which was genetically modified to express the MUC-CD antigenthereby better reflecting the majority of clinical ovarian tumor sampleswhich express the 4H11-targeted MUC-CD antigen (48). We initiallyverified specific lysis by MUC-CD targeted T cells demonstrating similarsignificant cytotoxic activity of 4H11z and 4H11-28z CAR modified Tcells targeting OV-CAR3(MUC-CD) tumor cells when compared control Tcells expressing the irrelevant first and second generationCD19-targeted 19z1 and 1928z CARs (FIG. 13A). Healthy donor T cellsmodified to express the 4H11-28z CAR similarly exhibited lysis offreshly isolated ascites derived MUC-CD⁺ ovarian carcinoma cells whencompared to 19-28z transduced T cells (FIG. 13B). Moreover, patient'speripheral blood T cells modified to express the 4H11-28z CAR similarlylysed autologous primary MUC-CD⁺ tumor cells derived from the sameascites sample when compared to T cells modified to express the control19-28z CAR (FIG. 13C).

We further assessed the ability of 4H11z⁺ and 4H11-28z⁺ T cells fromhealthy donors to proliferate following co-culture on OV-CAR3(MUC-CD) asassessed by FACS of CFSE labeled T cells, as well as absolute T cellsnumbers over 7 days following co-culture with tumor (FIGS. 13D and E).Surprisingly, we found that both 4H11z⁺ and 4H11-28z⁺ T cells expandedequally well following co-culture with OV-CAR3(MUC-CD) tumor cellssuggesting the ability of this tumor cell line to co-stimulate T cellsthrough expression of a co-stimulatory ligand. To address thispossibility, we conducted further FACS analyses of OV-CAR3(MUC-CD) tumorcells demonstrating expression of the co-stimulatory 4-1BBL ligand (FIG.13F), but not the B7. 1, B7.2, or OX-40L co-stimulatory ligands (datanot shown).

In Vivo Anti-Tumor Activity of MUC-CD Targeted T Cells in SCID-BeigeMice.

To assess the in vivo anti-tumor activity of 4H11z⁺ and 4H11-28z⁺ Tcells, we next generated an orthotopic xenotransplant ovarian cancertumor model by ip injection of OV-CAR3(MUC-CD) tumor cells intoSCID-Beige mice. If left untreated, these mice developed marked ascitesand multiple nodular peritoneal tumors by 3 weeks following tumor cellinjection (FIG. 14A). All untreated tumor bearing mice had to beeuthanized by 7 weeks following tumor cell injection due to evidence ofdistress.

To assess the in vivo anti-tumor efficacy of MUC-CD-targeted T cells,SCID-Beige mice were injected ip with OV-CAR3(MUC-CD/GFP-FFLuc) tumorcells on day 1 followed by ip injection of 4H11z⁺ or 4H11-28z⁺ T cellson day 2. For negative controls, tumor bearing mice were eitheruntreated or treated with T cells modified to express the irrelevantCD19-targeted CAR. Collectively, we found that 27% of all mice treatedwith MUC-CD targeted T cells (3/11 mice) remained alive without clinicalevidence of disease 120 days out from tumor injection with nostatistically significant difference in survival when comparing the4H11z⁺ and 4H11-28z⁺ T cell treated cohorts (FIG. 14B). In contrast,both MUC-CD-targeted T cell treated cohorts demonstrated statisticallysignificant enhanced survival when compared to untreated and 19z1⁺ Tcell treated control cohorts.

To assess whether systemically infused MUC-CD-targeted T cellssuccessfully traffic to ip tumors, we next compared ip to iv infusion of4H11-28z⁺ T cells in SCID-Beige mice bearing ipOV-CAR3(MUC-CD/GFP-FFLuc) tumors. Both ip and iv 4H11-28z⁺ T celltreated mice exhibited statistically enhanced survival when compared tountreated or 19-28z⁺ T cell treated control cohorts as assessed byoverall survival (FIG. 15A) as well as by BLI of tumor progression (FIG.15B). Furthermore, we found overall survival between the ip and ivtreated groups to be statistically equivalent by log rank analysis.These data imply successful trafficking of iv infused 4H11-28z⁺ T cellsto peritoneal tumors. We further confirmed trafficking of iv infusedCFSE labeled 4H11-28z⁺ T cells to the peritoneum by FACS analysis ofsingle cell suspensions of macerated OV-CAR3(MUC-CD) tumors (FIG. 15C).

In Vivo Anti-Tumor Activity of MUC-CD Targeted T Cells in SCID-BeigeMice Bearing Well Established OV-CAR3(MUC-CD/GFP-FFLuc) Tumors.

To further assess whether 4H11-28z⁺ T cells were able to eradicate moreclinically relevant tumor burdens, we next treated SCID-Beige micebearing well established ip OV-CAR3(MUC-CD/GFP-FFLuc) tumor injected 7days prior to adoptive T cell therapy. Once more, we found that therapywith MUC-CD targeted T cells markedly eradicated BLI evident disease inall treated mice (FIG. 16A) with 5 of 8 treated mice eventuallydeveloping relapsed progressive disease, and 3 mice remaining diseasefree as assessed by BLI imaging (not shown) out to 120 days post-tumorcell infusion (FIG. 16B). These data demonstrate potent in vivoanti-tumor activity mediated by MUC-CD targeted T cells even in thesetting of advanced disease.

Discussion

Based on extensive analyses of patient tumor samples, ovarian carcinomasappear to be relatively immunogenic tumors. Specifically, researchershave found there to be a direct correlation between prognosis followingsurgery and chemotherapy and the quantity of tumor infiltrating effectorT cells (TILs) in pretreatment tumor samples (25, 49, 50). Furthermore,others have described an inverse correlation between prognosis followingtherapy and pre-treatment levels of Tregs within the tumor, which inturn presumably inhibit the anti-tumor function of tumor specificeffector TILs (26, 28, 51). Both of these findings imply a role for anendogenous effector T cell response to tumor in controlling diseaseprogression both prior to and following initial therapy and stronglysupport the contention that ovarian carcinomas may be susceptible tokilling by adoptive infusion of autologous T cells targeted to ovariantumor cell antigens.

While endogenous effector TILs are one source for presumably tumorspecific T cells, an alternative approach to adoptive T cell therapy isto isolate autologous peripheral blood T cells which in turn may begenetically modified ex vivo to target tumor cell antigens. One suchgenetic approach is to retrovirally transduce patient T cells with CARstargeted to surface exposed antigens either unique to or over-expressedby the tumor. To this end, promising preclinical studies utilizing thisapproach in other malignancies have recently been translated into theclinical setting (6, 16, 19, 52). Similarly, we have previouslygenerated CARs targeted to the CD19 antigen expressed on normal B cellsas well as most B cell malignancies and are currently conductingclinical trials treating patients with relapsed B cell chroniclymphocytic leukemia and acute lymphoblastic leukemias with autologous Tcell modified to express a CD19 specific CAR (53).

Application of this approach to ovarian carcinomas requires theidentification to suitable target antigens expressed on the tumor cellsurface. Significantly, other investigators have studied this approachin both the pre-clinical and clinical setting (4, 11, 54-57).Specifically, several groups have demonstrated significant anti-tumorresponses to subcutaneous human ovarian carcinoma cell line tumors inimmune compromised mice following intratumoral and/or intravenousinfusion of T cells expressing CARs specific to the mesothelin andLewis-Y antigens overexpressed on these tumor cell lines (56, 58, 59).Furthermore, Kershaw et al recently published the results of a phase Iclinical trial treating patients with relapsed ovarian carcinomas withautologous T cells modified to express a CAR specific to thealpha-folate receptor (6). The authors of this study found that therapywith targeted T cells was well tolerated, but noted a lack of anti-tumorresponse in these studies related to poor persistence of modified Tcells over time as well as a yet undefined T cell inhibitory factor inthe serum of several treated patients.

In our studies, we have chosen to target the MUC-16 glycoprotein whichis over-expressed on a majority of ovarian carcinomas (1, 30, 32, 33).The utility of MUC-16 as a target antigen for adoptive T cell therapy iscompromised by the fact that most of the extracellular portion of thismolecule is cleaved by the tumor cell, secreted, and may be detected inthe serum as the CA-125 tumor marker. However, following cleavage ofthis secreted fraction of MUC-16, there remains a residual extracellularfraction of the glycoprotein, termed MUC-CD, which is retained on thetumor surface and is therefore an attractive target for immune-basedtherapies. To this end, we utilized a series of murine hybridomasgenerated to the MUC-CD antigen to construct CARs specific to MUC-CD. Ofthese CARs, we identified a CAR generated from the 4H11 murine hybridomatermed 4H11z, which, when expressed in human T cells, followingco-culture on 3T3(MUC-CD/B7.1) AAPCs, resulted in rapid destruction ofAAPC monolayers as well as marked modified T cell expansion.Significantly, the antigen to the 4H11 antibody is highly expressed on amajority of pre-treatment ovarian carcinoma surgical tumor samplesobtained from patients treated at our institution as assessed byimmuno-histochemistry (48).

Optimal T cell activation requires both a primary T cell receptormediated signal, “signal 1,” along with a co-stimulatory “signal 2.”Classically, this co-stimulatory signal may be provided by ligation ofeither B7.1 (CD80) or B7.2 (CD86) on the target cell with the T cellco-stimulatory receptor CD28. Alternatively, co-stimulation may begenerated by ligation of 4-1BBL or OX-40L on the target cell with therespective 4-1BB or OX40 co-stimulatory receptors on the T cell (12, 60,61). Since most tumor cells fail to express co-stimulatory ligands, weand others have previously demonstrated that second generation CARsfurther incorporating the cytoplasmic signaling domains theco-stimulatory receptors CD28, 4-1BB, and/or OX40 resulted in CARscapable of providing both signal 1 and signal 2 to the T cell uponbinding to cognate antigen in the absence of exogenous co-stimulatoryligands (7-10, 12, 13, 15, 16, 62-65). To this end, we constructed asecond generation CAR from the 4H11z CAR incorporating the transmembraneand cytoplasmic signaling domain of CD28 as described elsewhere (3, 9,43). Consistent with previous studies, we found that T cells transducedto express the resulting 4H11-28z CAR, but not the first generation4H11z CAR, efficiently expanded upon co-culture with 3T3(MUC-CD)fibroblasts in the absence of exogenous co-stimulation consistent withthe ability of the 4H11-28z CAR to deliver both signal 1 and signal 2 tothe T cell. This conclusion is further supported by the finding that4H11-28z⁺ T cells secreted significantly higher levels of IL-2, acytokine indicative of T cell co-stimulation, upon co-culture on3T3(MUC-CD) fibroblasts when compared to T cells transduced to expressthe first generation 4H11z CAR.

We next assessed the ability of 4H11z⁺ and 4H11-28z⁺ T cells to targetand lyse human ovarian carcinoma tumor cells. To this end, we initiallyutilized the OV-CAR3 human ovarian cancer cell line. Since the OV-CAR3tumor cell line binds the 4H11 antibody weakly, we further geneticallymodified the cell line to express MUC-CD (OV-CAR3(MUC-CD)) to bettermimic the clinical setting wherein a majority of clinical ovariancarcinoma tumor specimens highly express the 4H11 MUC-CD antigen (48).We demonstrated that human T cells modified to express either 4H11z⁺ or4H11-28z⁺ eradicated OV-CAR3(MUC-CD) tumor cells in vitro, andsurprisingly observed that both 4H11z⁺ and 4H11-28z⁺ T cells expandedfollowing co-culture with tumor in vitro. To define the etiology of thisunanticipated 4H11z⁺ T cell expansion, we further assessed whetherOV-CAR3(MUC-CD) tumor cells expressed co-stimulatory ligands, and foundthat this tumor cell line expressed 4-1BBL, consistent with ourexperimental findings as well as with previously published reportsdemonstrating 4-1BBL expression by a variety of carcinoma cell lines(66-68). In order to further validate the clinical relevance of thesefindings, we subsequently demonstrated specific in vitro lysis ofprimary ascites-derived tumor cells isolated from untreated ovariancarcinoma patients by both healthy donor allogeneic 4H11-28z⁺ T cells aswell as more significantly autologous 4H11-28z⁺ patient peripheral bloodT cells. These data strongly support the contention that treatment withautologous 4H11-based CAR⁺ T cells have promise in future clinicalapplications.

In order to assess the in vivo relevance of our in vitro findings, wenext generated a murine orthotopic OV-CAR3(MUC-CD) tumor model inSCID-Beige mice. We injected mice i.p. with OV-CAR3(MUC-CD) tumor cellsand the following day infused 4H11z⁺, 4H11-28z⁺, and control 19z1⁺ Tcells i.p. This treatment approach resulted in a significant but similardelay to tumor progression and long-term survival in both the 4H11z⁺ and4H11-28z⁺ T cell treated cohorts when compared to untreated mice or micetreated with control T cells targeted to the irrelevant CD19 antigen. Wenext compared ip to iv treatment with 4H11-28z⁺ T cells of orthotopicOV-CAR3(MUC-CD/GFP-FFLuc) bearing mice, and found similar statisticallysignificant survivals of mice over time with either direct ip infusionof T cells or systemic iv infusion of targeted T cells. Significantly,iv treated mice by day 1 following treatment, exhibited successfultrafficking of targeted T cells to the peritoneum. These data suggeststhat adoptive therapy with targeted T cells may be equally efficaciousfollowing either a direct infusion into the peritoneum or throughsystemic iv infusion. These findings further support the future clinicalpotential of this approach in treating patients both with local relapseof disease as well as metastatic relapse to sites outside of theperitoneum.

Finally, we assessed the ability of 4H11-28z⁺ T cells to eradicate moreestablished disease by delaying modified T cell ip infusion by 7 days,when mice had greater established tumor burdens as assessed bybioluminescent imaging. This experimental setting better reflects theinitial clinical setting wherein this adoptive T cell approach would beutilized. Significantly, despite the setting of markedly establisheddisease, 4H11-28z⁺ T cells retained the ability to lyse larger tumorburdens, delay relapse of tumor, and in a significant percentage ofmice, fully eradicate disease.

In the studies presented here, we have consistently utilized mixedpopulations of CD4⁺ and CD8⁺ CAR⁺ T cells to assess both in vitro and invivo anti-tumor activity. To this end, ongoing studies will address therole of isolated CD4⁺ and CD8⁺ CAR⁺ T cell subsets in the successfuleradication of disease in this SCID-Beige OV-CAR3(MUC-CD) tumor model.The results of these studies may have implications to translating thistherapeutic approach to the clinical setting. Furthermore, weacknowledge the limitations associated with the presented SCID-Beigetumor model. Namely, this is a xenotransplant model in an immunecompromised mouse. To this end, ongoing studies in or laboratory arefocused on generating a more clinically relevant syngeneic immunecompetent tumor model to better define the biology and anti-tumorefficacy of MUC-CD targeted CAR-modified T cells in the context of anintact immune system.

In conclusion, herein we present the first published data demonstratingthe feasibility of targeting MUC-16, an antigen over-expressed on amajority of ovarian carcinomas, through adoptive therapy withgenetically modified T cells targeted to the retained MUC-CD portion ofthe MUC-16 antigen. Further, this report is the first to demonstrateefficient targeting of T cells in an orthotopic, clinically relevant,murine model of ovarian cancer, demonstrating efficacy both by ip and ivinfusion of modified T cells. Finally, these data support the furthertranslation of this approach to the clinical setting in the form of aphase I clinical trial in patients with persistent or relapsed ovariancarcinomas following initial therapy with surgery and chemotherapy.

Example 5

Raising Mouse MUC16 Monoclonal Antibodies in Mice and Hamsters.

We selected 3 different regions of mouse MUC16 genome for whichmonoclonal antibodies were generated in mouse and hamster. The selectedregions of the mouse MUC16 are Peptide 1 (SEQ ID NO:21, ecto region ofcytoplasmic domain), Peptide 2 (SEQ ID NO:22, first cysteine loop) andPeptide 3 (SEQ ID NO:23, second cysteine loop) (FIG. 20A) and itscomparison with human MUC16 is shown in FIG. 20B. A cysteine was addedto the peptide sequence at the N terminus of Peptide 1 (SEQ ID NO:21)and Peptide 3 (SEQ ID NO:23) for better conjugation with KLH. Individualpeptides were conjugated to KLH using Promega kit. These 3 conjugatedpeptides were pooled and immunized into 5 mice and 4 hamsters. 5immunizations with a 3 week interval for each immunization wereadministered. Sera from these animals were tested by ELISA for theirspecific reactivity with individual peptides (SEQ ID NO:21, 22 and 23).Positive selected animals were allowed to rest for a month and then i.v.boosted with pooled peptides immunogen (SEQ ID NO:21, 22 and 23) andharvested the spleens after 4 days. Splenocytes were mixed withhybridoma partners and plated into microtiter plates at various clonaldensities. Plates were cultured at 37° C. 5% CO₂ for 10 days and thenselected the clones. Supernatants from these selected clones were testedby ELISA for their specific reactivity with individual peptides (SEQ IDNO:21, 22 and 23). Positive clonal sups were tested by FACS, westernblot and imaging using 2 mouse cell lines (ID8 and BR5-FVB1) and a humancell line (OVCAR-3).

Table 4 shows the summary of mouse and hamster monoclonal antibodiesagainst mouse MUC16 peptide antigens Peptide 1 (SEQ ID NO:21), Peptide 2(SEQ ID NO:22), and Peptide 3 (SEQ ID NO:23). A very strong antigenicresponse was seen with Peptide 1 (SEQ ID NO:21).

TABLE 4 Mouse Mouse MUC16 mAbs Frozen Mouse mAb Peptide 1 46  16(3-IgG1; 8-IgG2b; 1- IgM; 4-Unkown isotype) Peptide 2 0 0 Peptide 3 6 6(4-IgG1; 2-IgM) Peptide 1, 2, 3 0 0 Peptide 1, 2 0 0 Peptide 2, 3 0 0 NoPeptide 0 0 Mouse Hamster MUC16 mAbs Frozen Hamster mAb Peptide 1 69 21Peptide 2 6 6 Peptide 3 7 7 Peptide 1, 2, 3 2 1 Peptide 1, 2 1 1 Peptide2, 3 1 0 No Peptide 10 2 Animals not iv boosted with peptide 2Details of mouse and hamster mAbs against Peptide 1 (SEQ ID NO:21),Peptide 2 (SEQ ID NO:22), and Peptide 3 (SEQ ID NO:23 are listed inTable 5 and Table 6 respectively.

TABLE 5 Fusion isotype PEPTIDE Well Cloned Clones — 1 01D01 — 1 09F07IgG 1 1 16A09 no success — 1 21A07 — 1 24G10 IgG 1 1 10C04 yes 10C4-3H510C4-1F2 10C4-2H8 10C4-1G7 IgG 1 1 17F02 yes 17F2-3G5 17F2-3F6 17F2-2F917F2-1E11 IgG 2b 1 01A08 IgG 2b 1 01F08 IgG 1 12B10 yes 12B10-3F712B10-3G10 12B10-2F6 12B10-2F10 2b IgG 2b 1 17H10 IgG 2b 1 18D05 IgG 2b1 23B12 IgG 1 25E09 25E9-3 25E9-5 25E9-13 25E9-16 2b IgM 1 16F12 IgG 1 304A06 no success IgG 1 3 05D01 no success IgG 1 3 21B08 yes 21B8-1H1121B8-3G6 21B8-3H9 21B8-1G8 IgG 1 3 21E01 yes 21E1-1E3 21E1-1G9 21E1-2G721E1-3G12 IgM 3 08A02 IgM 3 13E05

TABLE 6 Hamster mAb Peptide Cloned 01H03 02F02 1 04E 4 04G07 1 04H01 34H1-2E1 4H1-2E3 4H1-3E1 4H1-3H3 06A08 1 06F02 1 07F08 3 07H05 2 09A0509E 1 3 09F08 1 09H10 10G06 1 10H11 1 11B10 1 12F09 2 15A08 1 15A8-15A8-2E10 15A8- 15A8-3D2 2E2 2E11 15H08 3 19B05 1 21H04 3 22B05 2 22B5-22B5-3G9 22B5- 22B5-3F11 1F6 2G8 22D11 3 23G12 1 25E 8 1 27H09 3 28B121&2&3 28C12 2 30H02 1 31A11 2 31C01 2 33H06 1&2 34F10 1 34H05 1 36C01 136C11 36E 4 1 37E 10 1 10H11 1

Hamster antibody 22B05 recognizes mouse (SEQ ID NO:22) and also thecorresponding human sequence (SEQ ID NO:15).

Western blot analysis using mouse ID8 and BR5-FVB1 cell extracts werealso performed for all the selected monoclonal antibodies as shown inFIG. 21 and FIG. 22 respectively.

Among the mouse MUC16 monoclonal antibodies, we selected 12B10-3G10subclone mouse mAb for further screening. Similarly, hamster monoclonalantibodies, 15A8-2E10, 22B5-2G8 and 4H1-2E1 subclones were selected forfurther screening.

Immunohistochemical analysis was performed with paraffin andcryosections of ID8 (mouse), OVCAR-3 (human), BR5-FVB1 (mouse) celllines and 13.5 days of Embryo. Paraffin or cryosections were probed withmouse 12B10 mAb, hamster 15A8, hamster 22B5 and hamster 4E1 mAbs to seethe early development of mouse MUC16 (FIGS. 23A-23B)

12B10-3G10 sub clone were further analyzed for single chain Fvfragments. FIG. 24 show 12B10-3G10 V_(H) and V_(L) DNA and Amino Acidssequences. Bioreactive supernatants and purified 12B10-3G10 weregenerated for animal studies and other characterization studies. FACSanalysis was performed with purified 12B10-3G10 on ID8, OVCAR3 andBR5-FVB1 cells showing over 90% positivity to both mouse and human MUC16ecto-domain fragment (FIG. 25).

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MICROORGANISM DEPOSIT

A hybridoma designated huMUC16Pep3-31A3.5, which produces the antibodydesignated 31A3 (also designated 31A3.5.1) in this specification, wasdeposited with the American Type Culture Collection (ATCC), located at10801 University Boulevard, Manassas, Va. 20110-2209, on Mar. 25, 2011,in compliance with the Budapest Treaty on the International Recognitionof the Deposit of Microorganisms for the Purposes of Patent Procedure,and was assigned ATCC Accession No. PTA-11773.

Each and every publication and patent mentioned in the abovespecification is herein incorporated by reference in its entirety forall purposes. Various modifications and variations of the describedmethods and system of the invention will be apparent to those skilled inthe art without departing from the scope and spirit of the invention.Although the invention has been described in connection with specificembodiments, the invention as claimed should not be unduly limited tosuch specific embodiments. Indeed, various modifications of thedescribed modes for carrying out the invention which are obvious tothose skilled in the art and in fields related thereto are intended tobe within the scope of the following claims.

We claim:
 1. An antibody or antigen-binding fragment thereof thatspecifically binds to a MUC16 polypeptide or to an antigenic portionthereof, wherein the MUC16 polypeptide is (SEQ ID NO: 02)TLDRSSVLVDGYSPNRNE,

and wherein the antibody comprises a variable heavy (“V_(H)”) chainencoded by SEQ ID NO:04 and a variable light (“V_(L)”) chain encoded bySEQ ID NO:05.
 2. The antibody or antigen-binding fragment of claim 1,wherein the antibody is a monoclonal antibody.
 3. The antibody orantigen-binding fragment of claim 1, wherein the antibody is a chimericantibody.
 4. A humanized antibody or antigen-binding fragment thereofmade by substituting the complementarity determining regions of a firstantibody into a human framework domain, wherein the humanized antibodyor antigen-binding fragment thereof specifically binds to a MUC16polypeptide or to an antigenic portion thereof, wherein the firstantibody specifically binds to the MUC16 polypeptide or the antigenicportion thereof, wherein the MUC16 polypeptide is TLDRSSVLVDGYSPNRNE(SEQ ID NO:02), and wherein the first antibody comprises a V_(H) chainencoded by SEQ ID NO:04 and a V_(L) chain encoded by SEQ ID NO:05. 5.The antibody or antigen-binding fragment of claim 4, whereinsubstantially all of the framework domain residues of the humanizedantibody are those of a human immunoglobulin sequence, and wherein oneor more of the framework domain residues are replaced by correspondingnonhuman residues.
 6. The antibody or antigen-binding fragment of claim1, wherein the antigen-binding fragment is selected from the groupconsisting of a Fab fragment, a F(ab′)₂ fragment, and a Fv fragment. 7.The antibody or antigen-binding fragment of claim 1, wherein theantibody or antigen-binding fragment is covalently linked to a cytotoxicagent or a prodrug of a cytotoxic agent.
 8. A composition comprising (a)the antibody or antigen-binding fragment of claim 1 and (b) apharmaceutically acceptable carrier.
 9. A composition comprising (a) theantibody or antigen-binding fragment of claim 4 and (b) apharmaceutically acceptable carrier.
 10. A hybridoma cell that producesa monoclonal antibody or an antigen-binding fragment thereof thatspecifically binds to the MUC16 polypeptide or to an antigen portionthereof, wherein the MUC16 polypeptide is (SEQ ID NO: 2)TLDRSSVLVDGYSPNRNE,

and wherein the antibody comprises a variable heavy (“VH”) chain encodedby SEQ ID NO:04 and a variable light (“VL”) chain encoded by SEQ IDNO:05.
 11. A method for identifying a subject as having a cancer inwhich MUC16 is expressed, wherein said method comprises administeringthe antibody of claim 1 the subject, and determining the presence andlocation of the antibody in the subject, wherein said antibody islabeled.
 12. A method for identifying a subject as having a cancer inwhich MUC16 is expressed, wherein said method comprises administeringthe antibody of claim 4 to the subject, and determining the presence andlocation of the antibody in the subject, wherein said antibody islabeled.
 13. The method of claim 11, wherein the cancer is selected fromthe group consisting of ovarian cancer and breast cancer.
 14. The methodof claim 12, wherein the cancer is selected from the group consisting ofovarian cancer and breast cancer.
 15. An ex vivo method for identifyinga subject as having a cancer in which MUC16 is expressed, wherein saidmethod comprises (a) obtaining a first sample from a first subject; (b)contacting the first sample with the antibody of claim 1; and (c)determining whether the antibody has an increased level of binding tothe first sample as compared to a control sample lacking the cancer. 16.The ex vivo method of claim 15, wherein the cancer is selected from thegroup consisting of ovarian cancer and breast cancer.
 17. An ex vivomethod for identifying a subject as having a cancer in which MUC16 isexpressed, wherein said method comprises (a) obtaining a first samplefrom a first subject; (b) contacting the first sample with the antibodyof claim 4; and (c) determining whether the antibody has an increasedlevel of binding to the first sample as compared to a control samplelacking the cancer.
 18. The ex vivo method of claim 17, wherein thecancer is selected from the group consisting of ovarian cancer andbreast cancer.
 19. A single chain variable fragment (scFv) comprising aVH chain sequence encoded by SEQ ID NO:04 and a VL chain sequenceencoded by SEQ ID NO:05.
 20. A single chain variable fragment (scFv)comprising a VH chain sequence and a VL chain sequence of the humanizedantibody or antigen-binding fragment of claim
 4. 21. A chimeric antigenreceptor (CAR) comprising the scFv of claim
 19. 22. A chimeric antigenreceptor (CAR) comprising the scFv of claim
 20. 23. A CAR comprising thescFv of claim 19 fused to a transmembrane domain.
 24. A CAR comprisingthe scFv of claim 20 to a transmembrane domain.
 25. The CAR of claim 23,wherein the transmembrane domain is fused to a T cell receptor ζ chaincytoplasmic signaling domain.
 26. The CAR of claim 24, wherein thetransmembrane domain is fused to a T cell receptor ζ chain cytoplasmicsignaling domain.
 27. The CAR of claim 25, further comprising acytoplasmic signaling domain of a co-stimulatory receptor, wherein theco-stimulatory receptor comprises CD28, 4-1BB, or OX40.
 28. The CAR ofclaim 26, further comprising a cytoplasmic signaling domain of aco-stimulatory receptor, wherein the co-stimulatory receptor comprisesCD28, 4-1BB, or OX40.
 29. The CAR of claim 23, comprising in amino- tocarboxy-terminal order: a human CD8 leader peptide, the scFv, a humanCD28 transmembrane domain and cytoplasmic signaling domain, and aCD3-zeta signaling domain.
 30. The CAR of claim 24, comprising in amino-to carboxy-terminal order: a human CD8 leader peptide, the scFv, a humanCD28 transmembrane domain and cytoplasmic signaling domain, and aCD3-zeta signaling domain.
 31. A T cell expressing the CAR of claim 21.32. A T cell expressing the CAR of claim
 22. 33. A method for treating acancer in which MUC16 is expressed, comprising administering to asubject the antibody or antigen binding fragment of claim
 1. 34. Amethod for treating a cancer in which MUC16 is expressed, comprisingadministering to a subject the antibody or antigen binding fragment ofclaim
 2. 35. A method for treating a cancer in which MUC16 is expressed,comprising administering to a subject the antibody or antigen bindingfragment of claim
 3. 36. A method for treating a cancer in which MUC16is expressed, comprising administering to a subject the antibody orantigen binding fragment of claim
 4. 37. A method for treating a cancerin which MUC16 is expressed, comprising administering to a subject theantibody or antigen binding fragment of claim
 5. 38. A method fortreating a cancer in which MUC16 is expressed, comprising administeringto a subject the antibody or antigen binding fragment of claim
 6. 39. Amethod for treating a cancer in which MUC16 is expressed, comprisingadministering to a subject the antibody or antigen binding fragment ofclaim
 7. 40. A method for treating a cancer in which MUC16 is expressed,comprising administering to a subject the T cell of claim
 31. 41. Amethod for treating a cancer in which MUC16 is expressed, comprisingadministering to a subject the T cell of claim
 32. 42. The method ofclaim 40, wherein the administering is intraperitoneally orintravenously.
 43. The method of claim 41, wherein the administering isintraperitoneally or intravenously.
 44. The method of claim 33, whereinthe cancer is selected from the group consisting of ovarian cancer andbreast cancer.
 45. The method of claim 34, wherein the cancer isselected from the group consisting of ovarian cancer and breast cancer.46. The method of claim 35, wherein the cancer is selected from thegroup consisting of ovarian cancer and breast cancer.
 47. The method ofclaim 36, wherein the cancer is selected from the group consisting ofovarian cancer and breast cancer.
 48. The method of claim 37, whereinthe cancer is selected from the group consisting of ovarian cancer andbreast cancer.
 49. The method of claim 38, wherein the cancer isselected from the group consisting of ovarian cancer and breast cancer.50. The method of claim 39, wherein the cancer is selected from thegroup consisting of ovarian cancer and breast cancer.
 51. The method ofclaim 40, wherein the cancer is selected from the group consisting ofovarian cancer and breast cancer.
 52. The method of claim 41, whereinthe cancer is selected from the group consisting of ovarian cancer andbreast cancer.
 53. The method of claim 23, which further comprisesdetecting a reduction in one or more symptoms of the cancer after theadministering step.
 54. A chimeric antibody that is the antibody ofclaim
 3. 55. A humanized antibody that is the antibody of claim
 4. 56. Amethod for treating a cancer in which MUC16 is expressed, comprisingadministering to a subject the antibody of claim
 54. 57. A method fortreating a cancer in which MUC16 is expressed, comprising administeringto a subject the antibody of claim 55.